Job ID = 6368376 SRX = SRX495056 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:03:45 prefetch.2.10.7: 1) Downloading 'SRR1198588'... 2020-06-16T00:03:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:06:22 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:06:22 prefetch.2.10.7: 1) 'SRR1198588' was downloaded successfully Read 17578572 spots for SRR1198588/SRR1198588.sra Written 17578572 spots for SRR1198588/SRR1198588.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: 00:02:38 17578572 reads; of these: 17578572 (100.00%) were unpaired; of these: 3758384 (21.38%) aligned 0 times 11528042 (65.58%) aligned exactly 1 time 2292146 (13.04%) aligned >1 times 78.62% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 7021545 / 13820188 = 0.5081 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 09:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.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 09:13:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:37: 1000000 INFO @ Tue, 16 Jun 2020 09:13:43: 2000000 INFO @ Tue, 16 Jun 2020 09:13:48: 3000000 INFO @ Tue, 16 Jun 2020 09:13:54: 4000000 INFO @ Tue, 16 Jun 2020 09:13:59: 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 09:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.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 09:14:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:05: 6000000 INFO @ Tue, 16 Jun 2020 09:14:09: 1000000 INFO @ Tue, 16 Jun 2020 09:14:09: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:09: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:09: #1 total tags in treatment: 6798643 INFO @ Tue, 16 Jun 2020 09:14:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:09: #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 09:14:10: #1 tags after filtering in treatment: 6798643 INFO @ Tue, 16 Jun 2020 09:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:10: #2 number of paired peaks: 542 WARNING @ Tue, 16 Jun 2020 09:14:10: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:10: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:14:10: #2 alternative fragment length(s) may be 2,43 bps INFO @ Tue, 16 Jun 2020 09:14:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.05_model.r WARNING @ Tue, 16 Jun 2020 09:14:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:14:10: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Tue, 16 Jun 2020 09:14:10: #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 09:14:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:14: 2000000 INFO @ Tue, 16 Jun 2020 09:14:20: 3000000 INFO @ Tue, 16 Jun 2020 09:14:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:27: 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 09:14:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.05_summits.bed INFO @ Tue, 16 Jun 2020 09:14:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (855 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.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 09:14:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:34: 5000000 INFO @ Tue, 16 Jun 2020 09:14:38: 1000000 INFO @ Tue, 16 Jun 2020 09:14:41: 6000000 INFO @ Tue, 16 Jun 2020 09:14:44: 2000000 INFO @ Tue, 16 Jun 2020 09:14:47: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:47: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:47: #1 total tags in treatment: 6798643 INFO @ Tue, 16 Jun 2020 09:14:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:47: #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 09:14:47: #1 tags after filtering in treatment: 6798643 INFO @ Tue, 16 Jun 2020 09:14:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:47: #2 number of paired peaks: 542 WARNING @ Tue, 16 Jun 2020 09:14:47: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:47: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:14:47: #2 alternative fragment length(s) may be 2,43 bps INFO @ Tue, 16 Jun 2020 09:14:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.10_model.r WARNING @ Tue, 16 Jun 2020 09:14:47: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:14:47: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Tue, 16 Jun 2020 09:14:47: #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 09:14:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:50: 3000000 INFO @ Tue, 16 Jun 2020 09:14:56: 4000000 INFO @ Tue, 16 Jun 2020 09:15:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:02: 5000000 INFO @ Tue, 16 Jun 2020 09:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.10_summits.bed INFO @ Tue, 16 Jun 2020 09:15:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (474 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:08: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:13: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:15:13: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:15:13: #1 total tags in treatment: 6798643 INFO @ Tue, 16 Jun 2020 09:15:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:13: #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 09:15:13: #1 tags after filtering in treatment: 6798643 INFO @ Tue, 16 Jun 2020 09:15:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:13: #2 number of paired peaks: 542 WARNING @ Tue, 16 Jun 2020 09:15:13: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:13: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:15:13: #2 alternative fragment length(s) may be 2,43 bps INFO @ Tue, 16 Jun 2020 09:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.20_model.r WARNING @ Tue, 16 Jun 2020 09:15:13: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:15:13: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Tue, 16 Jun 2020 09:15:13: #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 09:15:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:15:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495056/SRX495056.20_summits.bed INFO @ Tue, 16 Jun 2020 09:15:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling