Job ID = 6367387 SRX = SRX331146 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:21:31 prefetch.2.10.7: 1) Downloading 'SRR947377'... 2020-06-15T23:21:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:58 prefetch.2.10.7: 'SRR947377' is valid 2020-06-15T23:21:58 prefetch.2.10.7: 1) 'SRR947377' was downloaded successfully Read 5936673 spots for SRR947377/SRR947377.sra Written 5936673 spots for SRR947377/SRR947377.sra 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 Multiseed full-index search: 00:00:41 5936673 reads; of these: 5936673 (100.00%) were unpaired; of these: 3258132 (54.88%) aligned 0 times 2196637 (37.00%) aligned exactly 1 time 481904 (8.12%) aligned >1 times 45.12% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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_rmdupse_core] 110594 / 2678541 = 0.0413 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.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, 16 Jun 2020 08:24:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:08: 1000000 INFO @ Tue, 16 Jun 2020 08:24:14: 2000000 INFO @ Tue, 16 Jun 2020 08:24:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:24:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:24:18: #1 total tags in treatment: 2567947 INFO @ Tue, 16 Jun 2020 08:24:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:24:18: #1 tags after filtering in treatment: 2567947 INFO @ Tue, 16 Jun 2020 08:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:18: #2 number of paired peaks: 418 WARNING @ Tue, 16 Jun 2020 08:24:18: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:18: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:24:18: #2 alternative fragment length(s) may be 31,144,506,564,587 bps INFO @ Tue, 16 Jun 2020 08:24:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.05_model.r WARNING @ Tue, 16 Jun 2020 08:24:18: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:18: #2 You may need to consider one of the other alternative d(s): 31,144,506,564,587 WARNING @ Tue, 16 Jun 2020 08:24:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:24:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (319 records, 4 fields): 2 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:24:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.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, 16 Jun 2020 08:24:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:37: 1000000 INFO @ Tue, 16 Jun 2020 08:24:44: 2000000 INFO @ Tue, 16 Jun 2020 08:24:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:24:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:24:47: #1 total tags in treatment: 2567947 INFO @ Tue, 16 Jun 2020 08:24:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:24:47: #1 tags after filtering in treatment: 2567947 INFO @ Tue, 16 Jun 2020 08:24:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:48: #2 number of paired peaks: 418 WARNING @ Tue, 16 Jun 2020 08:24:48: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:48: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:24:48: #2 alternative fragment length(s) may be 31,144,506,564,587 bps INFO @ Tue, 16 Jun 2020 08:24:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.10_model.r WARNING @ Tue, 16 Jun 2020 08:24:48: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:48: #2 You may need to consider one of the other alternative d(s): 31,144,506,564,587 WARNING @ Tue, 16 Jun 2020 08:24:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:24:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.10_summits.bed INFO @ Tue, 16 Jun 2020 08:24:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:25:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.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, 16 Jun 2020 08:25:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:07: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:25:14: 2000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:18: #1 total tags in treatment: 2567947 INFO @ Tue, 16 Jun 2020 08:25:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:25:18: #1 tags after filtering in treatment: 2567947 INFO @ Tue, 16 Jun 2020 08:25:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:18: #2 number of paired peaks: 418 WARNING @ Tue, 16 Jun 2020 08:25:18: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:18: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:25:18: #2 alternative fragment length(s) may be 31,144,506,564,587 bps INFO @ Tue, 16 Jun 2020 08:25:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.20_model.r WARNING @ Tue, 16 Jun 2020 08:25:18: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:18: #2 You may need to consider one of the other alternative d(s): 31,144,506,564,587 WARNING @ Tue, 16 Jun 2020 08:25:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:25:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331146/SRX331146.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling