Job ID = 14160716 SRX = SRX10569204 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T18:52:13 prefetch.2.10.7: 1) Downloading 'SRR14202288'... 2021-12-08T18:52:13 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T18:53:19 prefetch.2.10.7: HTTPS download succeed 2021-12-08T18:53:19 prefetch.2.10.7: 1) 'SRR14202288' was downloaded successfully 2021-12-08T18:53:19 prefetch.2.10.7: 'SRR14202288' has 0 unresolved dependencies Read 18625705 spots for SRR14202288/SRR14202288.sra Written 18625705 spots for SRR14202288/SRR14202288.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160844 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:20 18625705 reads; of these: 18625705 (100.00%) were unpaired; of these: 5324798 (28.59%) aligned 0 times 10905022 (58.55%) aligned exactly 1 time 2395885 (12.86%) aligned >1 times 71.41% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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] 2219530 / 13300907 = 0.1669 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.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 @ Thu, 09 Dec 2021 04:04:57: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:04:57: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:05:03: 1000000 INFO @ Thu, 09 Dec 2021 04:05:10: 2000000 INFO @ Thu, 09 Dec 2021 04:05:16: 3000000 INFO @ Thu, 09 Dec 2021 04:05:22: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.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 @ Thu, 09 Dec 2021 04:05:27: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:05:27: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:05:29: 5000000 INFO @ Thu, 09 Dec 2021 04:05:33: 1000000 INFO @ Thu, 09 Dec 2021 04:05:35: 6000000 INFO @ Thu, 09 Dec 2021 04:05:39: 2000000 INFO @ Thu, 09 Dec 2021 04:05:41: 7000000 INFO @ Thu, 09 Dec 2021 04:05:45: 3000000 INFO @ Thu, 09 Dec 2021 04:05:48: 8000000 INFO @ Thu, 09 Dec 2021 04:05:51: 4000000 INFO @ Thu, 09 Dec 2021 04:05:54: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:05:56: 5000000 INFO @ Thu, 09 Dec 2021 04:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.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 @ Thu, 09 Dec 2021 04:05:57: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:05:57: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:06:01: 10000000 INFO @ Thu, 09 Dec 2021 04:06:02: 6000000 INFO @ Thu, 09 Dec 2021 04:06:04: 1000000 INFO @ Thu, 09 Dec 2021 04:06:07: 11000000 INFO @ Thu, 09 Dec 2021 04:06:08: 7000000 INFO @ Thu, 09 Dec 2021 04:06:08: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:06:08: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:06:08: #1 total tags in treatment: 11081377 INFO @ Thu, 09 Dec 2021 04:06:08: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:06:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:06:08: #1 tags after filtering in treatment: 11081377 INFO @ Thu, 09 Dec 2021 04:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:06:08: #1 finished! INFO @ Thu, 09 Dec 2021 04:06:08: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:06:09: #2 number of paired peaks: 328 WARNING @ Thu, 09 Dec 2021 04:06:09: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Thu, 09 Dec 2021 04:06:09: start model_add_line... INFO @ Thu, 09 Dec 2021 04:06:09: start X-correlation... INFO @ Thu, 09 Dec 2021 04:06:09: end of X-cor INFO @ Thu, 09 Dec 2021 04:06:09: #2 finished! INFO @ Thu, 09 Dec 2021 04:06:09: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 04:06:09: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 04:06:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.05_model.r WARNING @ Thu, 09 Dec 2021 04:06:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:06:09: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 04:06:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:06:09: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:06:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:06:10: 2000000 INFO @ Thu, 09 Dec 2021 04:06:14: 8000000 INFO @ Thu, 09 Dec 2021 04:06:17: 3000000 INFO @ Thu, 09 Dec 2021 04:06:19: 9000000 INFO @ Thu, 09 Dec 2021 04:06:24: 4000000 INFO @ Thu, 09 Dec 2021 04:06:25: 10000000 INFO @ Thu, 09 Dec 2021 04:06:29: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:06:30: 5000000 INFO @ Thu, 09 Dec 2021 04:06:31: 11000000 INFO @ Thu, 09 Dec 2021 04:06:32: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:06:32: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:06:32: #1 total tags in treatment: 11081377 INFO @ Thu, 09 Dec 2021 04:06:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:06:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:06:32: #1 tags after filtering in treatment: 11081377 INFO @ Thu, 09 Dec 2021 04:06:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:06:32: #1 finished! INFO @ Thu, 09 Dec 2021 04:06:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:06:32: #2 number of paired peaks: 328 WARNING @ Thu, 09 Dec 2021 04:06:32: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Thu, 09 Dec 2021 04:06:32: start model_add_line... INFO @ Thu, 09 Dec 2021 04:06:33: start X-correlation... INFO @ Thu, 09 Dec 2021 04:06:33: end of X-cor INFO @ Thu, 09 Dec 2021 04:06:33: #2 finished! INFO @ Thu, 09 Dec 2021 04:06:33: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 04:06:33: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 04:06:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.10_model.r WARNING @ Thu, 09 Dec 2021 04:06:33: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:06:33: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 04:06:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:06:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:06:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:06:37: 6000000 INFO @ Thu, 09 Dec 2021 04:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.05_summits.bed INFO @ Thu, 09 Dec 2021 04:06:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (604 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:06:43: 7000000 INFO @ Thu, 09 Dec 2021 04:06:49: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:06:52: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:06:55: 9000000 INFO @ Thu, 09 Dec 2021 04:07:02: 10000000 INFO @ Thu, 09 Dec 2021 04:07:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:07:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:07:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.10_summits.bed INFO @ Thu, 09 Dec 2021 04:07:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (387 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:07:09: 11000000 INFO @ Thu, 09 Dec 2021 04:07:09: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:07:09: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:07:09: #1 total tags in treatment: 11081377 INFO @ Thu, 09 Dec 2021 04:07:09: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:07:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:07:09: #1 tags after filtering in treatment: 11081377 INFO @ Thu, 09 Dec 2021 04:07:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:07:09: #1 finished! INFO @ Thu, 09 Dec 2021 04:07:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:07:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:07:10: #2 number of paired peaks: 328 WARNING @ Thu, 09 Dec 2021 04:07:10: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Thu, 09 Dec 2021 04:07:10: start model_add_line... INFO @ Thu, 09 Dec 2021 04:07:10: start X-correlation... INFO @ Thu, 09 Dec 2021 04:07:10: end of X-cor INFO @ Thu, 09 Dec 2021 04:07:10: #2 finished! INFO @ Thu, 09 Dec 2021 04:07:10: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 04:07:10: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 04:07:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.20_model.r WARNING @ Thu, 09 Dec 2021 04:07:10: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:07:10: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 04:07:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:07:10: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:07:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:07:31: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569204/SRX10569204.20_summits.bed INFO @ Thu, 09 Dec 2021 04:07:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 1 millis CompletedMACS2peakCalling