Job ID = 6367758 SRX = SRX4082372 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:47:44 prefetch.2.10.7: 1) Downloading 'SRR7164190'... 2020-06-15T23:47:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:27 prefetch.2.10.7: 'SRR7164190' is valid 2020-06-15T23:49:27 prefetch.2.10.7: 1) 'SRR7164190' was downloaded successfully 2020-06-15T23:49:27 prefetch.2.10.7: 'SRR7164190' has 0 unresolved dependencies Read 12482146 spots for SRR7164190/SRR7164190.sra Written 12482146 spots for SRR7164190/SRR7164190.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: 00:02:53 12482146 reads; of these: 12482146 (100.00%) were unpaired; of these: 1005878 (8.06%) aligned 0 times 8644543 (69.26%) aligned exactly 1 time 2831725 (22.69%) aligned >1 times 91.94% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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] 1818228 / 11476268 = 0.1584 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 08:56:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.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 08:56:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:15: 1000000 INFO @ Tue, 16 Jun 2020 08:56:21: 2000000 INFO @ Tue, 16 Jun 2020 08:56:27: 3000000 INFO @ Tue, 16 Jun 2020 08:56:33: 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 08:56:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.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 08:56:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:39: 5000000 INFO @ Tue, 16 Jun 2020 08:56:46: 1000000 INFO @ Tue, 16 Jun 2020 08:56:46: 6000000 INFO @ Tue, 16 Jun 2020 08:56:53: 7000000 INFO @ Tue, 16 Jun 2020 08:56:53: 2000000 INFO @ Tue, 16 Jun 2020 08:57:00: 8000000 INFO @ Tue, 16 Jun 2020 08:57:00: 3000000 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 08:57:07: 9000000 INFO @ Tue, 16 Jun 2020 08:57:07: 4000000 INFO @ Tue, 16 Jun 2020 08:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.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 08:57:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:11: #1 total tags in treatment: 9658040 INFO @ Tue, 16 Jun 2020 08:57:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:11: #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 08:57:11: #1 tags after filtering in treatment: 9658040 INFO @ Tue, 16 Jun 2020 08:57:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:12: #2 number of paired peaks: 465 WARNING @ Tue, 16 Jun 2020 08:57:12: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:12: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:57:12: #2 alternative fragment length(s) may be 2,46,569,590,594 bps INFO @ Tue, 16 Jun 2020 08:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.05_model.r WARNING @ Tue, 16 Jun 2020 08:57:12: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:12: #2 You may need to consider one of the other alternative d(s): 2,46,569,590,594 WARNING @ Tue, 16 Jun 2020 08:57:12: #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 08:57:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:14: 5000000 INFO @ Tue, 16 Jun 2020 08:57:15: 1000000 INFO @ Tue, 16 Jun 2020 08:57:21: 6000000 INFO @ Tue, 16 Jun 2020 08:57:22: 2000000 INFO @ Tue, 16 Jun 2020 08:57:29: 7000000 INFO @ Tue, 16 Jun 2020 08:57:30: 3000000 INFO @ Tue, 16 Jun 2020 08:57:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:36: 8000000 INFO @ Tue, 16 Jun 2020 08:57:37: 4000000 INFO @ Tue, 16 Jun 2020 08:57:43: 9000000 INFO @ Tue, 16 Jun 2020 08:57:44: 5000000 INFO @ Tue, 16 Jun 2020 08:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (938 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:47: #1 total tags in treatment: 9658040 INFO @ Tue, 16 Jun 2020 08:57:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:47: #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 08:57:48: #1 tags after filtering in treatment: 9658040 INFO @ Tue, 16 Jun 2020 08:57:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:48: #2 number of paired peaks: 465 WARNING @ Tue, 16 Jun 2020 08:57:48: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:48: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:57:48: #2 alternative fragment length(s) may be 2,46,569,590,594 bps INFO @ Tue, 16 Jun 2020 08:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.10_model.r WARNING @ Tue, 16 Jun 2020 08:57:48: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:48: #2 You may need to consider one of the other alternative d(s): 2,46,569,590,594 WARNING @ Tue, 16 Jun 2020 08:57:48: #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 08:57:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:50: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:57:56: 7000000 INFO @ Tue, 16 Jun 2020 08:58:03: 8000000 INFO @ Tue, 16 Jun 2020 08:58:09: 9000000 INFO @ Tue, 16 Jun 2020 08:58:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:58:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:58:13: #1 total tags in treatment: 9658040 INFO @ Tue, 16 Jun 2020 08:58:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:13: #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 08:58:13: #1 tags after filtering in treatment: 9658040 INFO @ Tue, 16 Jun 2020 08:58:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:14: #2 number of paired peaks: 465 WARNING @ Tue, 16 Jun 2020 08:58:14: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:14: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:58:14: #2 alternative fragment length(s) may be 2,46,569,590,594 bps INFO @ Tue, 16 Jun 2020 08:58:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.20_model.r WARNING @ Tue, 16 Jun 2020 08:58:14: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:58:14: #2 You may need to consider one of the other alternative d(s): 2,46,569,590,594 WARNING @ Tue, 16 Jun 2020 08:58:14: #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 08:58:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (436 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082372/SRX4082372.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (164 records, 4 fields): 2 millis CompletedMACS2peakCalling