Job ID = 6366734 SRX = SRX2228887 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:53 prefetch.2.10.7: 1) Downloading 'SRR4380343'... 2020-06-15T23:06:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:52 prefetch.2.10.7: 'SRR4380343' is valid 2020-06-15T23:07:52 prefetch.2.10.7: 1) 'SRR4380343' was downloaded successfully 2020-06-15T23:07:52 prefetch.2.10.7: 'SRR4380343' has 0 unresolved dependencies Read 10397250 spots for SRR4380343/SRR4380343.sra Written 10397250 spots for SRR4380343/SRR4380343.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: 00:02:26 10397250 reads; of these: 10397250 (100.00%) were unpaired; of these: 1347379 (12.96%) aligned 0 times 7497272 (72.11%) aligned exactly 1 time 1552599 (14.93%) aligned >1 times 87.04% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 1305326 / 9049871 = 0.1442 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 08:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.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 08:13:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:55: 1000000 INFO @ Tue, 16 Jun 2020 08:14:00: 2000000 INFO @ Tue, 16 Jun 2020 08:14:06: 3000000 INFO @ Tue, 16 Jun 2020 08:14:11: 4000000 INFO @ Tue, 16 Jun 2020 08:14:17: 5000000 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 08:14:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.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 08:14:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:23: 6000000 INFO @ Tue, 16 Jun 2020 08:14:25: 1000000 INFO @ Tue, 16 Jun 2020 08:14:29: 7000000 INFO @ Tue, 16 Jun 2020 08:14:31: 2000000 INFO @ Tue, 16 Jun 2020 08:14:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:33: #1 total tags in treatment: 7744545 INFO @ Tue, 16 Jun 2020 08:14:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:33: #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 08:14:33: #1 tags after filtering in treatment: 7744545 INFO @ Tue, 16 Jun 2020 08:14:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:34: #2 number of paired peaks: 462 WARNING @ Tue, 16 Jun 2020 08:14:34: Fewer paired peaks (462) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 462 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:34: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 08:14:34: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 16 Jun 2020 08:14:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.05_model.r WARNING @ Tue, 16 Jun 2020 08:14:34: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:34: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Tue, 16 Jun 2020 08:14:34: #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 08:14:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:37: 3000000 INFO @ Tue, 16 Jun 2020 08:14:43: 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 08:14:48: 5000000 INFO @ Tue, 16 Jun 2020 08:14:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.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 08:14:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:54: 6000000 INFO @ Tue, 16 Jun 2020 08:14:59: 1000000 INFO @ Tue, 16 Jun 2020 08:15:00: 7000000 INFO @ Tue, 16 Jun 2020 08:15:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1293 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:05: #1 total tags in treatment: 7744545 INFO @ Tue, 16 Jun 2020 08:15:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:05: #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 08:15:05: #1 tags after filtering in treatment: 7744545 INFO @ Tue, 16 Jun 2020 08:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:05: 2000000 INFO @ Tue, 16 Jun 2020 08:15:05: #2 number of paired peaks: 462 WARNING @ Tue, 16 Jun 2020 08:15:05: Fewer paired peaks (462) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 462 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:05: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 08:15:05: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 16 Jun 2020 08:15:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.10_model.r WARNING @ Tue, 16 Jun 2020 08:15:06: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:06: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Tue, 16 Jun 2020 08:15:06: #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 08:15:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:11: 3000000 INFO @ Tue, 16 Jun 2020 08:15:17: 4000000 INFO @ Tue, 16 Jun 2020 08:15:22: 5000000 INFO @ Tue, 16 Jun 2020 08:15:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:28: 6000000 INFO @ Tue, 16 Jun 2020 08:15:34: 7000000 INFO @ Tue, 16 Jun 2020 08:15:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (840 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:38: #1 total tags in treatment: 7744545 INFO @ Tue, 16 Jun 2020 08:15:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:38: #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 08:15:38: #1 tags after filtering in treatment: 7744545 INFO @ Tue, 16 Jun 2020 08:15:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:39: #2 number of paired peaks: 462 WARNING @ Tue, 16 Jun 2020 08:15:39: Fewer paired peaks (462) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 462 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:39: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 08:15:39: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 16 Jun 2020 08:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.20_model.r WARNING @ Tue, 16 Jun 2020 08:15:39: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:39: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Tue, 16 Jun 2020 08:15:39: #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 08:15:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228887/SRX2228887.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:08: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (401 records, 4 fields): 1 millis CompletedMACS2peakCalling