Job ID = 6507899 SRX = SRX495002 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:59:27 prefetch.2.10.7: 1) Downloading 'SRR1198534'... 2020-06-26T13:59:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:00:51 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:00:52 prefetch.2.10.7: 'SRR1198534' is valid 2020-06-26T14:00:52 prefetch.2.10.7: 1) 'SRR1198534' was downloaded successfully Read 13338445 spots for SRR1198534/SRR1198534.sra Written 13338445 spots for SRR1198534/SRR1198534.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: 00:02:43 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88329 (0.66%) aligned 0 times 10992955 (82.42%) aligned exactly 1 time 2257161 (16.92%) aligned >1 times 99.34% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 2114446 / 13250116 = 0.1596 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 23:07:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.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 23:07:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:07:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:07:55: 1000000 INFO @ Fri, 26 Jun 2020 23:08:00: 2000000 INFO @ Fri, 26 Jun 2020 23:08:06: 3000000 INFO @ Fri, 26 Jun 2020 23:08:12: 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 23:08:18: 5000000 INFO @ Fri, 26 Jun 2020 23:08:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.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 23:08:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:08:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:08:24: 6000000 INFO @ Fri, 26 Jun 2020 23:08:25: 1000000 INFO @ Fri, 26 Jun 2020 23:08:30: 7000000 INFO @ Fri, 26 Jun 2020 23:08:32: 2000000 INFO @ Fri, 26 Jun 2020 23:08:36: 8000000 INFO @ Fri, 26 Jun 2020 23:08:38: 3000000 INFO @ Fri, 26 Jun 2020 23:08:43: 9000000 INFO @ Fri, 26 Jun 2020 23:08:45: 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 @ Fri, 26 Jun 2020 23:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.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 23:08:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:08:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:08:49: 10000000 INFO @ Fri, 26 Jun 2020 23:08:51: 5000000 INFO @ Fri, 26 Jun 2020 23:08:56: 1000000 INFO @ Fri, 26 Jun 2020 23:08:56: 11000000 INFO @ Fri, 26 Jun 2020 23:08:57: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:08:57: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:08:57: #1 total tags in treatment: 11135670 INFO @ Fri, 26 Jun 2020 23:08:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:08:57: #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 23:08:57: #1 tags after filtering in treatment: 11135670 INFO @ Fri, 26 Jun 2020 23:08:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:08:57: #1 finished! INFO @ Fri, 26 Jun 2020 23:08:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:08:57: 6000000 INFO @ Fri, 26 Jun 2020 23:08:58: #2 number of paired peaks: 363 WARNING @ Fri, 26 Jun 2020 23:08:58: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Fri, 26 Jun 2020 23:08:58: start model_add_line... INFO @ Fri, 26 Jun 2020 23:08:58: start X-correlation... INFO @ Fri, 26 Jun 2020 23:08:58: end of X-cor INFO @ Fri, 26 Jun 2020 23:08:58: #2 finished! INFO @ Fri, 26 Jun 2020 23:08:58: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 23:08:58: #2 alternative fragment length(s) may be 2,40,593 bps INFO @ Fri, 26 Jun 2020 23:08:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.05_model.r WARNING @ Fri, 26 Jun 2020 23:08:58: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:08:58: #2 You may need to consider one of the other alternative d(s): 2,40,593 WARNING @ Fri, 26 Jun 2020 23:08:58: #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 23:08:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:08:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:09:02: 2000000 INFO @ Fri, 26 Jun 2020 23:09:04: 7000000 INFO @ Fri, 26 Jun 2020 23:09:09: 3000000 INFO @ Fri, 26 Jun 2020 23:09:10: 8000000 INFO @ Fri, 26 Jun 2020 23:09:16: 4000000 INFO @ Fri, 26 Jun 2020 23:09:17: 9000000 INFO @ Fri, 26 Jun 2020 23:09:22: 5000000 INFO @ Fri, 26 Jun 2020 23:09:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:09:23: 10000000 INFO @ Fri, 26 Jun 2020 23:09:29: 6000000 INFO @ Fri, 26 Jun 2020 23:09:30: 11000000 INFO @ Fri, 26 Jun 2020 23:09:31: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:09:31: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:09:31: #1 total tags in treatment: 11135670 INFO @ Fri, 26 Jun 2020 23:09:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:09:31: #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 23:09:31: #1 tags after filtering in treatment: 11135670 INFO @ Fri, 26 Jun 2020 23:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:09:31: #1 finished! INFO @ Fri, 26 Jun 2020 23:09:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:09:32: #2 number of paired peaks: 363 WARNING @ Fri, 26 Jun 2020 23:09:32: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Fri, 26 Jun 2020 23:09:32: start model_add_line... INFO @ Fri, 26 Jun 2020 23:09:32: start X-correlation... INFO @ Fri, 26 Jun 2020 23:09:32: end of X-cor INFO @ Fri, 26 Jun 2020 23:09:32: #2 finished! INFO @ Fri, 26 Jun 2020 23:09:32: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 23:09:32: #2 alternative fragment length(s) may be 2,40,593 bps INFO @ Fri, 26 Jun 2020 23:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.10_model.r WARNING @ Fri, 26 Jun 2020 23:09:32: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:09:32: #2 You may need to consider one of the other alternative d(s): 2,40,593 WARNING @ Fri, 26 Jun 2020 23:09:32: #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 23:09:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.05_summits.bed INFO @ Fri, 26 Jun 2020 23:09:35: Done! INFO @ Fri, 26 Jun 2020 23:09:35: 7000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (918 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:09:42: 8000000 INFO @ Fri, 26 Jun 2020 23:09:48: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:09:55: 10000000 INFO @ Fri, 26 Jun 2020 23:09:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:10:01: 11000000 INFO @ Fri, 26 Jun 2020 23:10:02: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:10:02: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:10:02: #1 total tags in treatment: 11135670 INFO @ Fri, 26 Jun 2020 23:10:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:10:02: #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 23:10:02: #1 tags after filtering in treatment: 11135670 INFO @ Fri, 26 Jun 2020 23:10:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:10:02: #1 finished! INFO @ Fri, 26 Jun 2020 23:10:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:10:03: #2 number of paired peaks: 363 WARNING @ Fri, 26 Jun 2020 23:10:03: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Fri, 26 Jun 2020 23:10:03: start model_add_line... INFO @ Fri, 26 Jun 2020 23:10:03: start X-correlation... INFO @ Fri, 26 Jun 2020 23:10:03: end of X-cor INFO @ Fri, 26 Jun 2020 23:10:03: #2 finished! INFO @ Fri, 26 Jun 2020 23:10:03: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 23:10:03: #2 alternative fragment length(s) may be 2,40,593 bps INFO @ Fri, 26 Jun 2020 23:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.20_model.r WARNING @ Fri, 26 Jun 2020 23:10:03: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:10:03: #2 You may need to consider one of the other alternative d(s): 2,40,593 WARNING @ Fri, 26 Jun 2020 23:10:03: #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 23:10:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:10:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:10:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.10_summits.bed INFO @ Fri, 26 Jun 2020 23:10:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:10:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:10:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:10:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:10:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495002/SRX495002.20_summits.bed INFO @ Fri, 26 Jun 2020 23:10:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 1 millis CompletedMACS2peakCalling