[?2004h(base) gskoksharova@genedev2:~$ samtools [?2004l Program: samtools (Tools for alignments in the SAM format) Version: 1.13 (using htslib 1.13+ds) Usage: samtools [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA fqidx index/extract FASTQ index index alignment -- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates ampliconclip clip oligos from the end of reads -- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA import Converts FASTA or FASTQ files to SAM/BAM/CRAM -- Statistics bedcov read depth per BED region coverage alignment depth and percent coverage depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck) ampliconstats generate amplicon specific stats -- Viewing flags explain BAM flags tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM -- Misc help [cmd] display this help message or help for [cmd] version detailed version information [?2004h(base) gskoksharova@genedev2:~$ samtools depth -b /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam -o /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test/txt.txt [?2004l [?2004h(base) gskoksharova@genedev2:~$ samtools depth -b /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam -o /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.txtMMM   MMMbedtools coverage -a /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed -b /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bed [?2004l Command 'bedtools' not found, but can be installed with: apt install bedtools [?2004h(base) gskoksharova@genedev2:~$ conda install bioconda::bedtools [?2004l Retrieving notices: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done Channels: - defaults - bioconda Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done Solving environment: | / done ## Package Plan ## environment location: /home/gskoksharova/miniconda3 added / updated specs: - bioconda::bedtools The following packages will be downloaded: package | build ---------------------------|----------------- bedtools-2.27.1 | h9a82719_5 702 KB bioconda ca-certificates-2025.7.15 | h06a4308_0 126 KB certifi-2025.8.3 | py312h06a4308_0 159 KB openssl-3.0.17 | h5eee18b_0 5.2 MB seqkit-2.10.1 | he881be0_0 11.8 MB bioconda ------------------------------------------------------------ Total: 17.9 MB The following NEW packages will be INSTALLED: bedtools bioconda/linux-64::bedtools-2.27.1-h9a82719_5 The following packages will be UPDATED: ca-certificates 2025.2.25-h06a4308_0 --> 2025.7.15-h06a4308_0 certifi 2025.6.15-py312h06a4308_0 --> 2025.8.3-py312h06a4308_0 openssl 3.0.16-h5eee18b_0 --> 3.0.17-h5eee18b_0 seqkit 2.10.0-h9ee0642_0 --> 2.10.1-he881be0_0 Proceed ([y]/n)? y Downloading and Extracting Packages: seqkit-2.10.1 | 11.8 MB | | 0% openssl-3.0.17 | 5.2 MB | | 0%  bedtools-2.27.1 | 702 KB | | 0%  certifi-2025.8.3 | 159 KB | | 0%  ca-certificates-2025 | 126 KB | | 0%  ca-certificates-2025 | 126 KB | ####7 | 13%  openssl-3.0.17 | 5.2 MB | 1 | 0%  certifi-2025.8.3 | 159 KB | ###7 | 10%  seqkit-2.10.1 | 11.8 MB | | 0% bedtools-2.27.1 | 702 KB | 8 | 2%  ca-certificates-2025 | 126 KB | ##################################### | 100%  ca-certificates-2025 | 126 KB | ##################################### | 100%  openssl-3.0.17 | 5.2 MB | 8 | 2%  seqkit-2.10.1 | 11.8 MB | 2 | 1% ca-certificates-2025 | 126 KB | ##################################### | 100%  certifi-2025.8.3 | 159 KB | #############################7 | 80%  certifi-2025.8.3 | 159 KB | ##################################### | 100%  bedtools-2.27.1 | 702 KB | #####9 | 16%  certifi-2025.8.3 | 159 KB | ##################################### | 100%  openssl-3.0.17 | 5.2 MB | ###3 | 9%  seqkit-2.10.1 | 11.8 MB | 6 | 2% bedtools-2.27.1 | 702 KB | ################8 | 46%  openssl-3.0.17 | 5.2 MB | #########2 | 25%  seqkit-2.10.1 | 11.8 MB | #7 | 5% bedtools-2.27.1 | 702 KB | ##################################### | 100%  openssl-3.0.17 | 5.2 MB | #########################5 | 69%  seqkit-2.10.1 | 11.8 MB | ####5 | 12% openssl-3.0.17 | 5.2 MB | ##################################### | 100%  seqkit-2.10.1 | 11.8 MB | ############ | 33% seqkit-2.10.1 | 11.8 MB | #########################2 | 68% bedtools-2.27.1 | 702 KB | ##################################### | 100%  bedtools-2.27.1 | 702 KB | ##################################### | 100%  openssl-3.0.17 | 5.2 MB | ##################################### | 100%  openssl-3.0.17 | 5.2 MB | ##################################### | 100%  seqkit-2.10.1 | 11.8 MB | ##################################### | 100% seqkit-2.10.1 | 11.8 MB | ##################################### | 100% seqkit-2.10.1 | 11.8 MB | ##################################### | 100%     Preparing transaction: \ done Verifying transaction: / - \ | / done Executing transaction: \ | / - done [?2004h(base) gskoksharova@genedev2:~$ conda install bioconda::bedtoolsbedtools coverage -a /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed -b /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bed [?2004l Killed [?2004h(base) gskoksharova@genedev2:~$ samtools coverage -r /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam -o /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.txt [?2004l samtools coverage: Failed to parse region "/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed". Check the region format or region name presence in the file "/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam" [?2004h(base) gskoksharova@genedev2:~$ samtools bedcov -c /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bed [?2004l bedcov: invalid option -- 'c' Usage: samtools bedcov [options] [...] Options: -Q mapping quality threshold [0] -X use customized index files -g remove the specified flags from the set used to filter out reads -G add the specified flags to the set used to filter out reads The default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704 -j do not include deletions (D) and ref skips (N) in bedcov computation -d depth threshold. Number of reference bases with coverage above and including this value will be displayed in a separate column --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] --verbosity INT Set level of verbosity [?2004h(base) gskoksharova@genedev2:~$ (base) gskoksharova@genedev2:~$ conda update samtools [?2004l PackageNotInstalledError: Package is not installed in prefix. prefix: /home/gskoksharova/miniconda3 package name: samtools [?2004h(base) gskoksharova@genedev2:~$ conda update samtoolssamtools bedcov -c /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bedM coverage -r /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam -o /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.txtM bedtools coverage -a /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed -b /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bedM conda install bioconda::bedtools Menv list [?2004l # conda environments: # base * /home/gskoksharova/miniconda3 tools /home/gskoksharova/miniconda3/envs/tools [?2004h(base) gskoksharova@genedev2:~$ conda activate tools [?2004l [?2004h(tools) gskoksharova@genedev2:~$ conda activate toolsenv listupdate samtoolssamtools [?2004l Program: samtools (Tools for alignments in the SAM format) Version: 1.13 (using htslib 1.13) Usage: samtools [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA fqidx index/extract FASTQ index index alignment -- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates ampliconclip clip oligos from the end of reads -- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA import Converts FASTA or FASTQ files to SAM/BAM/CRAM -- Statistics bedcov read depth per BED region coverage alignment depth and percent coverage depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck) ampliconstats generate amplicon specific stats -- Viewing flags explain BAM flags tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM -- Misc help [cmd] display this help message or help for [cmd] version detailed version information [?2004h(tools) gskoksharova@genedev2:~$ conda update samtools [?2004l Channels: - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done Solving environment: | / - done ## Package Plan ## environment location: /home/gskoksharova/miniconda3/envs/tools added / updated specs: - samtools The following packages will be UPDATED: ca-certificates 2024.11.26-h06a4308_0 --> 2025.7.15-h06a4308_0 Proceed ([y]/n)? y Downloading and Extracting Packages: Preparing transaction: - done Verifying transaction: | done Executing transaction: - done [?2004h(tools) gskoksharova@genedev2:~$ samtools [?2004l Program: samtools (Tools for alignments in the SAM format) Version: 1.13 (using htslib 1.13) Usage: samtools [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA fqidx index/extract FASTQ index index alignment -- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates ampliconclip clip oligos from the end of reads -- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA import Converts FASTA or FASTQ files to SAM/BAM/CRAM -- Statistics bedcov read depth per BED region coverage alignment depth and percent coverage depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck) ampliconstats generate amplicon specific stats -- Viewing flags explain BAM flags tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM -- Misc help [cmd] display this help message or help for [cmd] version detailed version information [?2004h(tools) gskoksharova@genedev2:~$ samtools bedcov [?2004l Usage: samtools bedcov [options] [...] Options: -Q mapping quality threshold [0] -X use customized index files -g remove the specified flags from the set used to filter out reads -G add the specified flags to the set used to filter out reads The default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704 -j do not include deletions (D) and ref skips (N) in bedcov computation -d depth threshold. Number of reference bases with coverage above and including this value will be displayed in a separate column --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] --verbosity INT Set level of verbosity [?2004h(tools) gskoksharova@genedev2:~$ conda install -c bioconda samtools [?2004l Channels: - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done Solving environment: - \ done # All requested packages already installed. [?2004h(tools) gskoksharova@genedev2:~$ conda install -c bioconda samtools==1.22.21 [?2004l Channels: - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / done Solving environment: \ | / - failed LibMambaUnsatisfiableError: Encountered problems while solving: - nothing provides libgcc >=13 needed by samtools-1.22.1-h96c455f_0 Could not solve for environment specs The following package could not be installed └─ samtools 1.22.1  is not installable because it requires └─ libgcc >=13 , which does not exist (perhaps a missing channel). [?2004h(tools) gskoksharova@genedev2:~$ conda install -c bioconda samtools==1.22.1 [?2004l Channels: - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / done Solving environment: \ | / - failed LibMambaUnsatisfiableError: Encountered problems while solving: - nothing provides libgcc >=13 needed by samtools-1.22-h96c455f_0 Could not solve for environment specs The following package could not be installed └─ samtools 1.22  is not installable because it requires └─ libgcc >=13 , which does not exist (perhaps a missing channel). [?2004h(tools) gskoksharova@genedev2:~$ conda install -c bioconda samtools==1.22 [?2004l Channels: - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done Solving environment: \ | done ## Package Plan ## environment location: /home/gskoksharova/miniconda3/envs/tools added / updated specs: - samtools==1.2 The following packages will be downloaded: package | build ---------------------------|----------------- samtools-1.2 | 2 1.3 MB bioconda ------------------------------------------------------------ Total: 1.3 MB The following packages will be DOWNGRADED: samtools 1.13-h8c37831_0 --> 1.2-2 Proceed ([y]/n)? n CondaSystemExit: Exiting. [?2004h(tools) gskoksharova@genedev2:~$ conda install -c bioconda samtools==1.20 [?2004l Channels: - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / done Solving environment: \ | / - failed LibMambaUnsatisfiableError: Encountered problems while solving: - nothing provides libgcc-ng >=12 needed by samtools-1.20-h50ea8bc_0 Could not solve for environment specs The following package could not be installed └─ samtools 1.20  is not installable because it requires └─ libgcc-ng >=12 , which does not exist (perhaps a missing channel). [?2004h(tools) gskoksharova@genedev2:~$ conda install -c bioconda samtools==1.2015 [?2004l Channels: - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / done Solving environment: \ | / - failed LibMambaUnsatisfiableError: Encountered problems while solving: - nothing provides libzlib >=1.2.11,<1.3.0a0 needed by samtools-1.15-h1170115_1 Could not solve for environment specs The following package could not be installed └─ samtools 1.15  is not installable because it requires └─ libzlib >=1.2.11,<1.3.0a0 , which does not exist (perhaps a missing channel). [?2004h(tools) gskoksharova@genedev2:~$ conda install -c bioconda samtools==1.15202.1samtools bedcovconda update samtoolssamtoolsconda activate toolsenv listupdate samtoolssamtools bedcov -c /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bed M /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batM /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batcM/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batchM [?2004l [?2004h(tools) gskoksharova@genedev2:~$ conda deactivate [?2004l [?2004h(base) gskoksharova@genedev2:~$ conda create -n samtools [?2004l Channels: - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / done Solving environment: \ done ## Package Plan ## environment location: /home/gskoksharova/miniconda3/envs/samtools Proceed ([y]/n)? y Downloading and Extracting Packages: Preparing transaction: - done Verifying transaction: | done Executing transaction: - done # # To activate this environment, use # # $ conda activate samtools # # To deactivate an active environment, use # # $ conda deactivate [?2004h(base) gskoksharova@genedev2:~$ conda activate samtools [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ conda activate samtools[1@create -ndeactivatesamtools bedcov /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bedM conda install -c bioconda samtools==1.15 M202.1 [?2004l Channels: - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - done Solving environment: | failed LibMambaUnsatisfiableError: Encountered problems while solving: - nothing provides libgcc >=13 needed by samtools-1.22-h96c455f_0 Could not solve for environment specs The following package could not be installed └─ samtools 1.22  is not installable because it requires └─ libgcc >=13 , which does not exist (perhaps a missing channel). [?2004h(samtools) gskoksharova@genedev2:~$ conda config --add channels bioconda [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ conda config --add channels conda-forge [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ conda config --add channels conda-forgebiocondainstall -c bioconda samtools==1.22activate samtoolsinstall -c bioconda samtools==1.22 samtools==1.22 samtools==1.22 samtools==1.22 samtools==1.22 samtools==1.22 samtools==1.22 samtools==1.22 samtools==1.22samtools==1.22 samtools==1.22 samtools==1.22samtools==1.22 [?2004l Channels: - conda-forge - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done Solving environment: / - done ## Package Plan ## environment location: /home/gskoksharova/miniconda3/envs/samtools added / updated specs: - samtools==1.22 The following packages will be downloaded: package | build ---------------------------|----------------- _libgcc_mutex-0.1 | conda_forge 3 KB conda-forge _openmp_mutex-4.5 | 2_gnu 23 KB conda-forge bzip2-1.0.8 | h4bc722e_7 247 KB conda-forge c-ares-1.34.5 | hb9d3cd8_0 202 KB conda-forge ca-certificates-2025.8.3 | hbd8a1cb_0 151 KB conda-forge htslib-1.22.1 | h566b1c6_0 3.1 MB bioconda keyutils-1.6.3 | hb9d3cd8_0 131 KB conda-forge krb5-1.21.3 | h659f571_0 1.3 MB conda-forge libcurl-8.14.1 | h332b0f4_0 439 KB conda-forge libdeflate-1.24 | h86f0d12_0 71 KB conda-forge libedit-3.1.20250104 | pl5321h7949ede_0 132 KB conda-forge libev-4.33 | hd590300_2 110 KB conda-forge libgcc-15.1.0 | h767d61c_4 805 KB conda-forge libgcc-ng-15.1.0 | h69a702a_4 29 KB conda-forge libgomp-15.1.0 | h767d61c_4 437 KB conda-forge liblzma-5.8.1 | hb9d3cd8_2 110 KB conda-forge libnghttp2-1.64.0 | h161d5f1_0 632 KB conda-forge libssh2-1.11.1 | hcf80075_0 298 KB conda-forge libstdcxx-15.1.0 | h8f9b012_4 3.7 MB conda-forge libstdcxx-ng-15.1.0 | h4852527_4 29 KB conda-forge libzlib-1.3.1 | hb9d3cd8_2 60 KB conda-forge ncurses-6.5 | h2d0b736_3 871 KB conda-forge openssl-3.5.2 | h26f9b46_0 3.0 MB conda-forge samtools-1.22 | h96c455f_0 490 KB bioconda zstd-1.5.7 | hb8e6e7a_2 554 KB conda-forge ------------------------------------------------------------ Total: 16.8 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 c-ares conda-forge/linux-64::c-ares-1.34.5-hb9d3cd8_0 ca-certificates conda-forge/noarch::ca-certificates-2025.8.3-hbd8a1cb_0 htslib bioconda/linux-64::htslib-1.22.1-h566b1c6_0 keyutils conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0 krb5 conda-forge/linux-64::krb5-1.21.3-h659f571_0 libcurl conda-forge/linux-64::libcurl-8.14.1-h332b0f4_0 libdeflate conda-forge/linux-64::libdeflate-1.24-h86f0d12_0 libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 libev conda-forge/linux-64::libev-4.33-hd590300_2 libgcc conda-forge/linux-64::libgcc-15.1.0-h767d61c_4 libgcc-ng conda-forge/linux-64::libgcc-ng-15.1.0-h69a702a_4 libgomp conda-forge/linux-64::libgomp-15.1.0-h767d61c_4 liblzma conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2 libnghttp2 conda-forge/linux-64::libnghttp2-1.64.0-h161d5f1_0 libssh2 conda-forge/linux-64::libssh2-1.11.1-hcf80075_0 libstdcxx conda-forge/linux-64::libstdcxx-15.1.0-h8f9b012_4 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-15.1.0-h4852527_4 libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3 openssl conda-forge/linux-64::openssl-3.5.2-h26f9b46_0 samtools bioconda/linux-64::samtools-1.22-h96c455f_0 zstd conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2 Proceed ([y]/n)? y Downloading and Extracting Packages: libstdcxx-15.1.0 | 3.7 MB | | 0% htslib-1.22.1 | 3.1 MB | | 0%  openssl-3.5.2 | 3.0 MB | | 0%  krb5-1.21.3 | 1.3 MB | | 0%  ncurses-6.5 | 871 KB | | 0%  libgcc-15.1.0 | 805 KB | | 0%  libnghttp2-1.64.0 | 632 KB | | 0% 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Executing transaction: / - \ | / - \ | / - \ | / - \ | / done [?2004h(samtools) gskoksharova@genedev2:~$ samtools [?2004l Program: samtools (Tools for alignments in the SAM format) Version: 1.22 (using htslib 1.22.1) Usage: samtools [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA fqidx index/extract FASTQ index index alignment -- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates ampliconclip clip oligos from the end of reads -- File operations collate shuffle and group alignments by name cat concatenate BAMs consensus produce a consensus Pileup/FASTA/FASTQ merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA import Converts FASTA or FASTQ files to SAM/BAM/CRAM reference Generates a reference from aligned data reset Reverts aligner changes in reads -- Statistics bedcov read depth per BED region coverage alignment depth and percent coverage depth compute the depth flagstat simple stats idxstats BAM index stats cram-size list CRAM Content-ID and Data-Series sizes phase phase heterozygotes stats generate stats (former bamcheck) ampliconstats generate amplicon specific stats checksum produce order-agnostic checksums of sequence content -- Viewing flags explain BAM flags head header viewer tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM samples list the samples in a set of SAM/BAM/CRAM files -- Misc help [cmd] display this help message or help for [cmd] version detailed version information [?2004h(samtools) gskoksharova@genedev2:~$ 0samtoolsconda install samtools==1.22config --add channels conda-forgebiocondainstall -c bioconda samtools==1.22activate samtools[1@create -ndeactivatesamtools bedcov /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bedM conda install -c bioconda samtools==1.15 M samtools bedcov /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bedM conda install -c bioconda samtools==1.15 M202.1samtools bedcov [?2004l Usage: samtools bedcov [options] [...] Options: -Q, --min-MQ mapping quality threshold [0] -X use customized index files -g remove the specified flags from the set used to filter out reads -G add the specified flags to the set used to filter out reads The default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704 -j do not include deletions (D) and ref skips (N) in bedcov computation --max-depth sets the maximum depth used in the mpileup algorithm -d depth threshold. Number of reference bases with coverage above and including this value will be displayed in a separate column -c add an additional column showing read count -H print a comment/header line with column information. --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] --verbosity INT Set level of verbosity [?2004h(samtools) gskoksharova@genedev2:~$ samtools bedcovconda install samtools==1.22config --add channels conda-forgebiocondainstall -c bioconda samtools==1.22activate samtools[1@create -ndeactivatesamtools bedcov /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bedM conda install -c bioconda samtools==1.15 M202.1samtools bedcovconda update samtoolssamtoolsconda activate toolsenv listupdate samtoolssamtools bedcov -c /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bed [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ (samtools) gskoksharova@genedev2:~$ samtools bedcov -c /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/test.bedMMM   MMMsamtools bedcov /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/1-25_R1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/1-25_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/1-36_R1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/1-36_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/63-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/142Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/146-1_R1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/146-1_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/146-1_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/146-2_R1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/146-2_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/149-1_R1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/149-1_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/149-3_R1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/149-3_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/149-4_R1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/149-4_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/151-4_R1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/151-4_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/151-9_R1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/151-9_R2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/181-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/181-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/27110-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/27110-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/d9987w-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/d9987w-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_143-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/NPC_146-7-2Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/NPC_controls.bed [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ samtools bedcov /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP5Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP43-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP43-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP63-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP142Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP143Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP146-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP146-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP146-Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP149-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP149-3Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP149-4Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP151-4Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP151-9Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iPS27110Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iTAF_1-25Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iTAF_1-36Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iTAF_2-3Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/d9987Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/IPSC_controls.bed [?2004l [E::hts_open_format] Failed to open file "/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP146-Aligned.out.sorted.bam" : No such file or directory ERROR: fail to open index BAM file '/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP146-Aligned.out.sorted.bam' [?2004h(samtools) gskoksharova@genedev2:~$ samtools bedcov /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP5Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP43-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP43-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP63-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP142Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP143Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP146-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP146-2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP146-7Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP149-1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP149-3Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP149-4Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP151-4Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iP151-9Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iPS27110Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iTAF_1-25Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iTAF_1-36Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/iTAF_2-3Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/d9987Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/IPSC_controls.bed [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ samtools bedcov /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/STAG_exons.bed /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/A1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/A2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/A3Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/B1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/C1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/C2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/D1Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/D2Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/D3Aligned.out.sorted.bam /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/D4Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/coverage/IPSC_clones.bed Md [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ (samtools) gskoksharova@genedev2:~$ for sample in iP5 iP43-1 iP43-2 iP63-2 iP142 iP143 iP146-1 iP146-2 iP146-7 iP149-1 iP149-3 iP149-4 iP151-4 iP151-9 iPS27110 iTAF_1-25 iTAF_1-36 iTAF_2-3 d9987; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/1_2batch/${sample}.txt; doene [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ for sample in A1 A2 B1 C1 C2 D1 D2 D3 D4; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txt; done [?2004l [?2004h(samtools) gskoksharova@genedev2:~$ for sample in A1 A2 B1 C1 C2 D1 D2 D3 D4; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txt; done M M M; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6bMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6baMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batcMMM; do samtols flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batchMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/MMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/$MMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${MMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${saMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${samMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sampMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${samplMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sampleMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}MMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.MMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.tMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txtMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txt; doneMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txt; doneMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txt; doneMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txt; doneMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txt; doneMMM; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txt; doneMMM3; do samtools flagstat /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}Aligned.out.sorted.bam > /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/6batch/${sample}.txt; doneMMM [?2004l [?2004h(samtools) gskoksharova@genedev2:~$