Job ID = 16436146 SRX = SRX9091667 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Warning: skipping mate #1 of read 'SRR12608192.10901862 10901862 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.10901862 10901862 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.13425390 13425390 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.13425390 13425390 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.27592083 27592083 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.27592083 27592083 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.28215486 28215486 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.28215486 28215486 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.32198105 32198105 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.32198105 32198105 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.41029738 41029738 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.41029738 41029738 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.41085364 41085364 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.41085364 41085364 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.42828026 42828026 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.42828026 42828026 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.44607797 44607797 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.44607797 44607797 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.46246401 46246401 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.46246401 46246401 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608192.48526455 48526455 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608192.48526455 48526455 length=1' because it was < 2 characters long Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 40 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 44527627 / 45636861 = 0.9757 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:32:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 12:32:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:32:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:32:09: 1000000 INFO @ Tue, 02 Aug 2022 12:32:16: 2000000 INFO @ Tue, 02 Aug 2022 12:32:24: 3000000 INFO @ Tue, 02 Aug 2022 12:32:25: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 12:32:25: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 12:32:25: #1 total tags in treatment: 1084661 INFO @ Tue, 02 Aug 2022 12:32:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:32:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:32:25: #1 tags after filtering in treatment: 689249 INFO @ Tue, 02 Aug 2022 12:32:25: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 12:32:25: #1 finished! INFO @ Tue, 02 Aug 2022 12:32:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:32:26: #2 number of paired peaks: 1437 INFO @ Tue, 02 Aug 2022 12:32:26: start model_add_line... INFO @ Tue, 02 Aug 2022 12:32:26: start X-correlation... INFO @ Tue, 02 Aug 2022 12:32:26: end of X-cor INFO @ Tue, 02 Aug 2022 12:32:26: #2 finished! INFO @ Tue, 02 Aug 2022 12:32:26: #2 predicted fragment length is 122 bps INFO @ Tue, 02 Aug 2022 12:32:26: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 02 Aug 2022 12:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.05_model.r WARNING @ Tue, 02 Aug 2022 12:32:26: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:32:26: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Tue, 02 Aug 2022 12:32:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:32:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:32:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:32:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.05_summits.bed INFO @ Tue, 02 Aug 2022 12:32:29: Done! WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (690 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:32:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 12:32:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:32:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:32:39: 1000000 INFO @ Tue, 02 Aug 2022 12:32:47: 2000000 INFO @ Tue, 02 Aug 2022 12:32:54: 3000000 INFO @ Tue, 02 Aug 2022 12:32:56: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 12:32:56: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 12:32:56: #1 total tags in treatment: 1084661 INFO @ Tue, 02 Aug 2022 12:32:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:32:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:32:56: #1 tags after filtering in treatment: 689249 INFO @ Tue, 02 Aug 2022 12:32:56: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 12:32:56: #1 finished! INFO @ Tue, 02 Aug 2022 12:32:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:32:56: #2 number of paired peaks: 1437 INFO @ Tue, 02 Aug 2022 12:32:56: start model_add_line... INFO @ Tue, 02 Aug 2022 12:32:56: start X-correlation... INFO @ Tue, 02 Aug 2022 12:32:56: end of X-cor INFO @ Tue, 02 Aug 2022 12:32:56: #2 finished! INFO @ Tue, 02 Aug 2022 12:32:56: #2 predicted fragment length is 122 bps INFO @ Tue, 02 Aug 2022 12:32:56: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 02 Aug 2022 12:32:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.10_model.r WARNING @ Tue, 02 Aug 2022 12:32:56: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:32:56: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Tue, 02 Aug 2022 12:32:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:32:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:32:58: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.10_summits.bed INFO @ Tue, 02 Aug 2022 12:32:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (502 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:33:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 12:33:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:33:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:33:10: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:33:18: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:33:26: 3000000 INFO @ Tue, 02 Aug 2022 12:33:27: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 12:33:27: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 12:33:27: #1 total tags in treatment: 1084661 INFO @ Tue, 02 Aug 2022 12:33:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:33:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:33:27: #1 tags after filtering in treatment: 689249 INFO @ Tue, 02 Aug 2022 12:33:27: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 12:33:27: #1 finished! INFO @ Tue, 02 Aug 2022 12:33:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:33:27: #2 number of paired peaks: 1437 INFO @ Tue, 02 Aug 2022 12:33:27: start model_add_line... INFO @ Tue, 02 Aug 2022 12:33:27: start X-correlation... INFO @ Tue, 02 Aug 2022 12:33:27: end of X-cor INFO @ Tue, 02 Aug 2022 12:33:27: #2 finished! INFO @ Tue, 02 Aug 2022 12:33:27: #2 predicted fragment length is 122 bps INFO @ Tue, 02 Aug 2022 12:33:27: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 02 Aug 2022 12:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.20_model.r WARNING @ Tue, 02 Aug 2022 12:33:27: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:33:27: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Tue, 02 Aug 2022 12:33:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:33:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:33:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091667/SRX9091667.20_summits.bed INFO @ Tue, 02 Aug 2022 12:33:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (276 records, 4 fields): 17 millis CompletedMACS2peakCalling