Job ID = 6507855 SRX = SRX494938 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:46:17 prefetch.2.10.7: 1) Downloading 'SRR1198470'... 2020-06-26T12:46:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:48:25 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:48:25 prefetch.2.10.7: 1) 'SRR1198470' was downloaded successfully Read 24995798 spots for SRR1198470/SRR1198470.sra Written 24995798 spots for SRR1198470/SRR1198470.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: 00:05:41 24995798 reads; of these: 24995798 (100.00%) were unpaired; of these: 1671623 (6.69%) aligned 0 times 18899387 (75.61%) aligned exactly 1 time 4424788 (17.70%) aligned >1 times 93.31% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 3919207 / 23324175 = 0.1680 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 22:01:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.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 22:01:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:01:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:01:16: 1000000 INFO @ Fri, 26 Jun 2020 22:01:23: 2000000 INFO @ Fri, 26 Jun 2020 22:01:28: 3000000 INFO @ Fri, 26 Jun 2020 22:01:34: 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 @ Fri, 26 Jun 2020 22:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.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 22:01:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:01:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:01:40: 5000000 INFO @ Fri, 26 Jun 2020 22:01:47: 1000000 INFO @ Fri, 26 Jun 2020 22:01:47: 6000000 INFO @ Fri, 26 Jun 2020 22:01:53: 2000000 INFO @ Fri, 26 Jun 2020 22:01:53: 7000000 INFO @ Fri, 26 Jun 2020 22:01:59: 3000000 INFO @ Fri, 26 Jun 2020 22:02:00: 8000000 INFO @ Fri, 26 Jun 2020 22:02:05: 4000000 INFO @ Fri, 26 Jun 2020 22:02:06: 9000000 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 @ Fri, 26 Jun 2020 22:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.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 22:02:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:02:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:02:12: 5000000 INFO @ Fri, 26 Jun 2020 22:02:13: 10000000 INFO @ Fri, 26 Jun 2020 22:02:17: 1000000 INFO @ Fri, 26 Jun 2020 22:02:18: 6000000 INFO @ Fri, 26 Jun 2020 22:02:19: 11000000 INFO @ Fri, 26 Jun 2020 22:02:23: 2000000 INFO @ Fri, 26 Jun 2020 22:02:25: 7000000 INFO @ Fri, 26 Jun 2020 22:02:26: 12000000 INFO @ Fri, 26 Jun 2020 22:02:29: 3000000 INFO @ Fri, 26 Jun 2020 22:02:31: 8000000 INFO @ Fri, 26 Jun 2020 22:02:32: 13000000 INFO @ Fri, 26 Jun 2020 22:02:36: 4000000 INFO @ Fri, 26 Jun 2020 22:02:38: 9000000 INFO @ Fri, 26 Jun 2020 22:02:38: 14000000 INFO @ Fri, 26 Jun 2020 22:02:42: 5000000 INFO @ Fri, 26 Jun 2020 22:02:44: 10000000 INFO @ Fri, 26 Jun 2020 22:02:44: 15000000 INFO @ Fri, 26 Jun 2020 22:02:48: 6000000 INFO @ Fri, 26 Jun 2020 22:02:50: 11000000 INFO @ Fri, 26 Jun 2020 22:02:51: 16000000 INFO @ Fri, 26 Jun 2020 22:02:55: 7000000 INFO @ Fri, 26 Jun 2020 22:02:56: 12000000 INFO @ Fri, 26 Jun 2020 22:02:57: 17000000 INFO @ Fri, 26 Jun 2020 22:03:01: 8000000 INFO @ Fri, 26 Jun 2020 22:03:02: 13000000 INFO @ Fri, 26 Jun 2020 22:03:04: 18000000 INFO @ Fri, 26 Jun 2020 22:03:08: 9000000 INFO @ Fri, 26 Jun 2020 22:03:09: 14000000 INFO @ Fri, 26 Jun 2020 22:03:10: 19000000 INFO @ Fri, 26 Jun 2020 22:03:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:03:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:03:12: #1 total tags in treatment: 19404968 INFO @ Fri, 26 Jun 2020 22:03:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:03:12: #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 22:03:13: #1 tags after filtering in treatment: 19404968 INFO @ Fri, 26 Jun 2020 22:03:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:03:13: #1 finished! INFO @ Fri, 26 Jun 2020 22:03:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:03:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:03:14: 10000000 INFO @ Fri, 26 Jun 2020 22:03:14: #2 number of paired peaks: 237 WARNING @ Fri, 26 Jun 2020 22:03:14: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Fri, 26 Jun 2020 22:03:14: start model_add_line... INFO @ Fri, 26 Jun 2020 22:03:14: start X-correlation... INFO @ Fri, 26 Jun 2020 22:03:14: end of X-cor INFO @ Fri, 26 Jun 2020 22:03:14: #2 finished! INFO @ Fri, 26 Jun 2020 22:03:14: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 22:03:14: #2 alternative fragment length(s) may be 1,37,49,559 bps INFO @ Fri, 26 Jun 2020 22:03:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.05_model.r WARNING @ Fri, 26 Jun 2020 22:03:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:03:14: #2 You may need to consider one of the other alternative d(s): 1,37,49,559 WARNING @ Fri, 26 Jun 2020 22:03:14: #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 22:03:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:03:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:03:15: 15000000 INFO @ Fri, 26 Jun 2020 22:03:20: 11000000 INFO @ Fri, 26 Jun 2020 22:03:21: 16000000 INFO @ Fri, 26 Jun 2020 22:03:26: 12000000 INFO @ Fri, 26 Jun 2020 22:03:27: 17000000 INFO @ Fri, 26 Jun 2020 22:03:32: 13000000 INFO @ Fri, 26 Jun 2020 22:03:34: 18000000 INFO @ Fri, 26 Jun 2020 22:03:39: 14000000 INFO @ Fri, 26 Jun 2020 22:03:40: 19000000 INFO @ Fri, 26 Jun 2020 22:03:42: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:03:42: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:03:42: #1 total tags in treatment: 19404968 INFO @ Fri, 26 Jun 2020 22:03:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:03:42: #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 22:03:43: #1 tags after filtering in treatment: 19404968 INFO @ Fri, 26 Jun 2020 22:03:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:03:43: #1 finished! INFO @ Fri, 26 Jun 2020 22:03:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:03:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:03:44: #2 number of paired peaks: 237 WARNING @ Fri, 26 Jun 2020 22:03:44: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Fri, 26 Jun 2020 22:03:44: start model_add_line... INFO @ Fri, 26 Jun 2020 22:03:44: start X-correlation... INFO @ Fri, 26 Jun 2020 22:03:44: end of X-cor INFO @ Fri, 26 Jun 2020 22:03:44: #2 finished! INFO @ Fri, 26 Jun 2020 22:03:44: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 22:03:44: #2 alternative fragment length(s) may be 1,37,49,559 bps INFO @ Fri, 26 Jun 2020 22:03:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.10_model.r WARNING @ Fri, 26 Jun 2020 22:03:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:03:44: #2 You may need to consider one of the other alternative d(s): 1,37,49,559 WARNING @ Fri, 26 Jun 2020 22:03:44: #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 22:03:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:03:45: 15000000 INFO @ Fri, 26 Jun 2020 22:03:51: 16000000 INFO @ Fri, 26 Jun 2020 22:03:52: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:03:57: 17000000 INFO @ Fri, 26 Jun 2020 22:04:02: 18000000 INFO @ Fri, 26 Jun 2020 22:04:08: 19000000 INFO @ Fri, 26 Jun 2020 22:04:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.05_summits.bed INFO @ Fri, 26 Jun 2020 22:04:10: Done! INFO @ Fri, 26 Jun 2020 22:04:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:04:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:04:10: #1 total tags in treatment: 19404968 INFO @ Fri, 26 Jun 2020 22:04:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:04:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (947 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:04:11: #1 tags after filtering in treatment: 19404968 INFO @ Fri, 26 Jun 2020 22:04:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:04:11: #1 finished! INFO @ Fri, 26 Jun 2020 22:04:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:04:12: #2 number of paired peaks: 237 WARNING @ Fri, 26 Jun 2020 22:04:12: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Fri, 26 Jun 2020 22:04:12: start model_add_line... INFO @ Fri, 26 Jun 2020 22:04:12: start X-correlation... INFO @ Fri, 26 Jun 2020 22:04:12: end of X-cor INFO @ Fri, 26 Jun 2020 22:04:12: #2 finished! INFO @ Fri, 26 Jun 2020 22:04:12: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 22:04:12: #2 alternative fragment length(s) may be 1,37,49,559 bps INFO @ Fri, 26 Jun 2020 22:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.20_model.r WARNING @ Fri, 26 Jun 2020 22:04:12: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:04:12: #2 You may need to consider one of the other alternative d(s): 1,37,49,559 WARNING @ Fri, 26 Jun 2020 22:04:12: #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 22:04:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:04:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:04:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:04:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:04:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.10_summits.bed INFO @ Fri, 26 Jun 2020 22:04:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:04:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:05:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:05:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:05:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494938/SRX494938.20_summits.bed INFO @ Fri, 26 Jun 2020 22:05:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 1 millis CompletedMACS2peakCalling