Job ID = 6367695 SRX = SRX3942558 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:35 prefetch.2.10.7: 1) Downloading 'SRR7010079'... 2020-06-15T23:34:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:25 prefetch.2.10.7: 'SRR7010079' is valid 2020-06-15T23:37:25 prefetch.2.10.7: 1) 'SRR7010079' was downloaded successfully 2020-06-15T23:37:25 prefetch.2.10.7: 'SRR7010079' has 0 unresolved dependencies Read 16902415 spots for SRR7010079/SRR7010079.sra Written 16902415 spots for SRR7010079/SRR7010079.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: 00:06:01 16902415 reads; of these: 16902415 (100.00%) were unpaired; of these: 1403349 (8.30%) aligned 0 times 12522660 (74.09%) aligned exactly 1 time 2976406 (17.61%) aligned >1 times 91.70% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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 8 files... [bam_rmdupse_core] 2966487 / 15499066 = 0.1914 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 08:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.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 08:48:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:39: 1000000 INFO @ Tue, 16 Jun 2020 08:48:45: 2000000 INFO @ Tue, 16 Jun 2020 08:48:51: 3000000 INFO @ Tue, 16 Jun 2020 08:48:57: 4000000 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 08:49:02: 5000000 INFO @ Tue, 16 Jun 2020 08:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.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 08:49:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:09: 6000000 INFO @ Tue, 16 Jun 2020 08:49:10: 1000000 INFO @ Tue, 16 Jun 2020 08:49:15: 7000000 INFO @ Tue, 16 Jun 2020 08:49:16: 2000000 INFO @ Tue, 16 Jun 2020 08:49:21: 8000000 INFO @ Tue, 16 Jun 2020 08:49:22: 3000000 INFO @ Tue, 16 Jun 2020 08:49:28: 9000000 INFO @ Tue, 16 Jun 2020 08:49:29: 4000000 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 08:49:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.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 08:49:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:35: 10000000 INFO @ Tue, 16 Jun 2020 08:49:36: 5000000 INFO @ Tue, 16 Jun 2020 08:49:41: 1000000 INFO @ Tue, 16 Jun 2020 08:49:42: 11000000 INFO @ Tue, 16 Jun 2020 08:49:43: 6000000 INFO @ Tue, 16 Jun 2020 08:49:49: 12000000 INFO @ Tue, 16 Jun 2020 08:49:49: 2000000 INFO @ Tue, 16 Jun 2020 08:49:50: 7000000 INFO @ Tue, 16 Jun 2020 08:49:52: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:49:52: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:49:52: #1 total tags in treatment: 12532579 INFO @ Tue, 16 Jun 2020 08:49:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:52: #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 08:49:53: #1 tags after filtering in treatment: 12532579 INFO @ Tue, 16 Jun 2020 08:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:53: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:49:53: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:54: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 08:49:54: #2 alternative fragment length(s) may be 2,64 bps INFO @ Tue, 16 Jun 2020 08:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.05_model.r WARNING @ Tue, 16 Jun 2020 08:49:54: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:54: #2 You may need to consider one of the other alternative d(s): 2,64 WARNING @ Tue, 16 Jun 2020 08:49:54: #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 08:49:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:57: 3000000 INFO @ Tue, 16 Jun 2020 08:49:57: 8000000 INFO @ Tue, 16 Jun 2020 08:50:04: 9000000 INFO @ Tue, 16 Jun 2020 08:50:04: 4000000 INFO @ Tue, 16 Jun 2020 08:50:11: 10000000 INFO @ Tue, 16 Jun 2020 08:50:12: 5000000 INFO @ Tue, 16 Jun 2020 08:50:18: 11000000 INFO @ Tue, 16 Jun 2020 08:50:19: 6000000 INFO @ Tue, 16 Jun 2020 08:50:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:25: 12000000 INFO @ Tue, 16 Jun 2020 08:50:27: 7000000 INFO @ Tue, 16 Jun 2020 08:50:28: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:50:28: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:50:28: #1 total tags in treatment: 12532579 INFO @ Tue, 16 Jun 2020 08:50:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:28: #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 08:50:29: #1 tags after filtering in treatment: 12532579 INFO @ Tue, 16 Jun 2020 08:50:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:29: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:50:29: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:29: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 08:50:29: #2 alternative fragment length(s) may be 2,64 bps INFO @ Tue, 16 Jun 2020 08:50:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:30: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:30: #2 You may need to consider one of the other alternative d(s): 2,64 WARNING @ Tue, 16 Jun 2020 08:50:30: #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 08:50:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1734 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:34: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:41: 9000000 INFO @ Tue, 16 Jun 2020 08:50:48: 10000000 INFO @ Tue, 16 Jun 2020 08:50:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:55: 11000000 INFO @ Tue, 16 Jun 2020 08:51:02: 12000000 INFO @ Tue, 16 Jun 2020 08:51:05: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:51:05: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:51:05: #1 total tags in treatment: 12532579 INFO @ Tue, 16 Jun 2020 08:51:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:06: #1 tags after filtering in treatment: 12532579 INFO @ Tue, 16 Jun 2020 08:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:06: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:51:06: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:07: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 08:51:07: #2 alternative fragment length(s) may be 2,64 bps INFO @ Tue, 16 Jun 2020 08:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:07: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:07: #2 You may need to consider one of the other alternative d(s): 2,64 WARNING @ Tue, 16 Jun 2020 08:51:07: #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 08:51:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (515 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942558/SRX3942558.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 1 millis CompletedMACS2peakCalling