Job ID = 6368242 SRX = SRX494925 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:20 prefetch.2.10.7: 1) Downloading 'SRR1198457'... 2020-06-16T00:14:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:22 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:22 prefetch.2.10.7: 1) 'SRR1198457' was downloaded successfully Read 15695316 spots for SRR1198457/SRR1198457.sra Written 15695316 spots for SRR1198457/SRR1198457.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: 00:03:33 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1826656 (11.64%) aligned 0 times 11335164 (72.22%) aligned exactly 1 time 2533496 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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] 1281866 / 13868660 = 0.0924 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 09:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.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 09:24:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:47: 1000000 INFO @ Tue, 16 Jun 2020 09:24:54: 2000000 INFO @ Tue, 16 Jun 2020 09:25:00: 3000000 INFO @ Tue, 16 Jun 2020 09:25:06: 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 09:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.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 09:25:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:12: 5000000 INFO @ Tue, 16 Jun 2020 09:25:18: 1000000 INFO @ Tue, 16 Jun 2020 09:25:19: 6000000 INFO @ Tue, 16 Jun 2020 09:25:24: 2000000 INFO @ Tue, 16 Jun 2020 09:25:26: 7000000 INFO @ Tue, 16 Jun 2020 09:25:31: 3000000 INFO @ Tue, 16 Jun 2020 09:25:33: 8000000 INFO @ Tue, 16 Jun 2020 09:25:38: 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 09:25:39: 9000000 INFO @ Tue, 16 Jun 2020 09:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.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 09:25:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:45: 5000000 INFO @ Tue, 16 Jun 2020 09:25:46: 10000000 INFO @ Tue, 16 Jun 2020 09:25:50: 1000000 INFO @ Tue, 16 Jun 2020 09:25:52: 6000000 INFO @ Tue, 16 Jun 2020 09:25:54: 11000000 INFO @ Tue, 16 Jun 2020 09:25:58: 2000000 INFO @ Tue, 16 Jun 2020 09:25:59: 7000000 INFO @ Tue, 16 Jun 2020 09:26:01: 12000000 INFO @ Tue, 16 Jun 2020 09:26:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:26:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:26:05: #1 total tags in treatment: 12586794 INFO @ Tue, 16 Jun 2020 09:26:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:05: #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 09:26:05: #1 tags after filtering in treatment: 12586794 INFO @ Tue, 16 Jun 2020 09:26:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:06: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 09:26:06: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:06: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:26:06: #2 alternative fragment length(s) may be 2,47,522,541,543 bps INFO @ Tue, 16 Jun 2020 09:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.05_model.r WARNING @ Tue, 16 Jun 2020 09:26:06: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:06: #2 You may need to consider one of the other alternative d(s): 2,47,522,541,543 WARNING @ Tue, 16 Jun 2020 09:26:06: #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 09:26:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:07: 8000000 INFO @ Tue, 16 Jun 2020 09:26:07: 3000000 INFO @ Tue, 16 Jun 2020 09:26:14: 9000000 INFO @ Tue, 16 Jun 2020 09:26:15: 4000000 INFO @ Tue, 16 Jun 2020 09:26:21: 10000000 INFO @ Tue, 16 Jun 2020 09:26:22: 5000000 INFO @ Tue, 16 Jun 2020 09:26:28: 11000000 INFO @ Tue, 16 Jun 2020 09:26:30: 6000000 INFO @ Tue, 16 Jun 2020 09:26:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:36: 12000000 INFO @ Tue, 16 Jun 2020 09:26:38: 7000000 INFO @ Tue, 16 Jun 2020 09:26:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:26:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:26:40: #1 total tags in treatment: 12586794 INFO @ Tue, 16 Jun 2020 09:26:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:40: #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 09:26:40: #1 tags after filtering in treatment: 12586794 INFO @ Tue, 16 Jun 2020 09:26:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:41: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 09:26:41: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:41: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:26:41: #2 alternative fragment length(s) may be 2,47,522,541,543 bps INFO @ Tue, 16 Jun 2020 09:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:41: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:41: #2 You may need to consider one of the other alternative d(s): 2,47,522,541,543 WARNING @ Tue, 16 Jun 2020 09:26:41: #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 09:26:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (664 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:46: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:26:53: 9000000 INFO @ Tue, 16 Jun 2020 09:27:00: 10000000 INFO @ Tue, 16 Jun 2020 09:27:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:08: 11000000 INFO @ Tue, 16 Jun 2020 09:27:15: 12000000 INFO @ Tue, 16 Jun 2020 09:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.10_summits.bed INFO @ Tue, 16 Jun 2020 09:27:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (498 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:27:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:27:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:27:19: #1 total tags in treatment: 12586794 INFO @ Tue, 16 Jun 2020 09:27:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:19: #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 09:27:19: #1 tags after filtering in treatment: 12586794 INFO @ Tue, 16 Jun 2020 09:27:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:20: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 09:27:20: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:20: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:27:20: #2 alternative fragment length(s) may be 2,47,522,541,543 bps INFO @ Tue, 16 Jun 2020 09:27:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.20_model.r WARNING @ Tue, 16 Jun 2020 09:27:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:20: #2 You may need to consider one of the other alternative d(s): 2,47,522,541,543 WARNING @ Tue, 16 Jun 2020 09:27:20: #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 09:27:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494925/SRX494925.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling