Job ID = 6497525 SRX = SRX495115 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:33:34 prefetch.2.10.7: 1) Downloading 'SRR1198647'... 2020-06-25T22:33:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:38:08 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:38:08 prefetch.2.10.7: 1) 'SRR1198647' was downloaded successfully Read 30872377 spots for SRR1198647/SRR1198647.sra Written 30872377 spots for SRR1198647/SRR1198647.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: 00:07:11 30872377 reads; of these: 30872377 (100.00%) were unpaired; of these: 5278118 (17.10%) aligned 0 times 21033782 (68.13%) aligned exactly 1 time 4560477 (14.77%) aligned >1 times 82.90% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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 12 files... [bam_rmdupse_core] 12231870 / 25594259 = 0.4779 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 @ Fri, 26 Jun 2020 07:53:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.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 @ Fri, 26 Jun 2020 07:53:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:53:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:53:31: 1000000 INFO @ Fri, 26 Jun 2020 07:53:39: 2000000 INFO @ Fri, 26 Jun 2020 07:53:47: 3000000 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 @ Fri, 26 Jun 2020 07:53:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.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 @ Fri, 26 Jun 2020 07:53:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:53:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:53:56: 4000000 INFO @ Fri, 26 Jun 2020 07:54:01: 1000000 INFO @ Fri, 26 Jun 2020 07:54:04: 5000000 INFO @ Fri, 26 Jun 2020 07:54:09: 2000000 INFO @ Fri, 26 Jun 2020 07:54:12: 6000000 INFO @ Fri, 26 Jun 2020 07:54:17: 3000000 BedGraph に変換中... INFO @ Fri, 26 Jun 2020 07:54:21: 7000000 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 @ Fri, 26 Jun 2020 07:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.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 @ Fri, 26 Jun 2020 07:54:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:54:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:54:25: 4000000 INFO @ Fri, 26 Jun 2020 07:54:29: 8000000 INFO @ Fri, 26 Jun 2020 07:54:33: 1000000 INFO @ Fri, 26 Jun 2020 07:54:33: 5000000 INFO @ Fri, 26 Jun 2020 07:54:38: 9000000 INFO @ Fri, 26 Jun 2020 07:54:41: 6000000 INFO @ Fri, 26 Jun 2020 07:54:42: 2000000 INFO @ Fri, 26 Jun 2020 07:54:47: 10000000 INFO @ Fri, 26 Jun 2020 07:54:49: 7000000 INFO @ Fri, 26 Jun 2020 07:54:51: 3000000 INFO @ Fri, 26 Jun 2020 07:54:55: 11000000 INFO @ Fri, 26 Jun 2020 07:54:57: 8000000 INFO @ Fri, 26 Jun 2020 07:54:59: 4000000 INFO @ Fri, 26 Jun 2020 07:55:04: 12000000 INFO @ Fri, 26 Jun 2020 07:55:05: 9000000 INFO @ Fri, 26 Jun 2020 07:55:08: 5000000 INFO @ Fri, 26 Jun 2020 07:55:12: 13000000 INFO @ Fri, 26 Jun 2020 07:55:13: 10000000 INFO @ Fri, 26 Jun 2020 07:55:15: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:55:15: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:55:15: #1 total tags in treatment: 13362389 INFO @ Fri, 26 Jun 2020 07:55:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:55:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:55:15: #1 tags after filtering in treatment: 13362389 INFO @ Fri, 26 Jun 2020 07:55:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:55:15: #1 finished! INFO @ Fri, 26 Jun 2020 07:55:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:55:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:55:16: #2 number of paired peaks: 311 WARNING @ Fri, 26 Jun 2020 07:55:16: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Fri, 26 Jun 2020 07:55:16: start model_add_line... INFO @ Fri, 26 Jun 2020 07:55:17: start X-correlation... INFO @ Fri, 26 Jun 2020 07:55:17: end of X-cor INFO @ Fri, 26 Jun 2020 07:55:17: #2 finished! INFO @ Fri, 26 Jun 2020 07:55:17: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 07:55:17: #2 alternative fragment length(s) may be 3,53 bps INFO @ Fri, 26 Jun 2020 07:55:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.05_model.r WARNING @ Fri, 26 Jun 2020 07:55:17: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:55:17: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Fri, 26 Jun 2020 07:55:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:55:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:55:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:55:17: 6000000 INFO @ Fri, 26 Jun 2020 07:55:21: 11000000 INFO @ Fri, 26 Jun 2020 07:55:26: 7000000 INFO @ Fri, 26 Jun 2020 07:55:29: 12000000 INFO @ Fri, 26 Jun 2020 07:55:34: 8000000 INFO @ Fri, 26 Jun 2020 07:55:36: 13000000 INFO @ Fri, 26 Jun 2020 07:55:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:55:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:55:39: #1 total tags in treatment: 13362389 INFO @ Fri, 26 Jun 2020 07:55:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:55:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:55:39: #1 tags after filtering in treatment: 13362389 INFO @ Fri, 26 Jun 2020 07:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:55:39: #1 finished! INFO @ Fri, 26 Jun 2020 07:55:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:55:41: #2 number of paired peaks: 311 WARNING @ Fri, 26 Jun 2020 07:55:41: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Fri, 26 Jun 2020 07:55:41: start model_add_line... INFO @ Fri, 26 Jun 2020 07:55:41: start X-correlation... INFO @ Fri, 26 Jun 2020 07:55:41: end of X-cor INFO @ Fri, 26 Jun 2020 07:55:41: #2 finished! INFO @ Fri, 26 Jun 2020 07:55:41: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 07:55:41: #2 alternative fragment length(s) may be 3,53 bps INFO @ Fri, 26 Jun 2020 07:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.10_model.r WARNING @ Fri, 26 Jun 2020 07:55:41: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:55:41: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Fri, 26 Jun 2020 07:55:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:55:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:55:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:55:43: 9000000 INFO @ Fri, 26 Jun 2020 07:55:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:55:51: 10000000 INFO @ Fri, 26 Jun 2020 07:55:59: 11000000 INFO @ Fri, 26 Jun 2020 07:56:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:56:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:56:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.05_summits.bed INFO @ Fri, 26 Jun 2020 07:56:07: Done! INFO @ Fri, 26 Jun 2020 07:56:07: 12000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1782 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:56:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:56:15: 13000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:56:18: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:56:18: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:56:18: #1 total tags in treatment: 13362389 INFO @ Fri, 26 Jun 2020 07:56:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:56:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:56:18: #1 tags after filtering in treatment: 13362389 INFO @ Fri, 26 Jun 2020 07:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:56:18: #1 finished! INFO @ Fri, 26 Jun 2020 07:56:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:56:19: #2 number of paired peaks: 311 WARNING @ Fri, 26 Jun 2020 07:56:19: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Fri, 26 Jun 2020 07:56:19: start model_add_line... INFO @ Fri, 26 Jun 2020 07:56:19: start X-correlation... INFO @ Fri, 26 Jun 2020 07:56:19: end of X-cor INFO @ Fri, 26 Jun 2020 07:56:19: #2 finished! INFO @ Fri, 26 Jun 2020 07:56:19: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 07:56:19: #2 alternative fragment length(s) may be 3,53 bps INFO @ Fri, 26 Jun 2020 07:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.20_model.r WARNING @ Fri, 26 Jun 2020 07:56:19: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:56:19: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Fri, 26 Jun 2020 07:56:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:56:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:56:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:56:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:56:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.10_summits.bed INFO @ Fri, 26 Jun 2020 07:56:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (547 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:56:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:57:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:57:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:57:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495115/SRX495115.20_summits.bed INFO @ Fri, 26 Jun 2020 07:57:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 5 millis CompletedMACS2peakCalling