Job ID = 14171281 SRX = SRX9986133 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14786455 spots for SRR13591552/SRR13591552.sra Written 14786455 spots for SRR13591552/SRR13591552.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171726 ("srTdm6") 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: 00:04:45 14786455 reads; of these: 14786455 (100.00%) were unpaired; of these: 699705 (4.73%) aligned 0 times 9409284 (63.63%) aligned exactly 1 time 4677466 (31.63%) aligned >1 times 95.27% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1507937 / 14086750 = 0.1070 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 @ Sat, 11 Dec 2021 11:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 11 Dec 2021 11:00:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:00:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:00:12: 1000000 INFO @ Sat, 11 Dec 2021 11:00:17: 2000000 INFO @ Sat, 11 Dec 2021 11:00:21: 3000000 INFO @ Sat, 11 Dec 2021 11:00:26: 4000000 INFO @ Sat, 11 Dec 2021 11:00:30: 5000000 INFO @ Sat, 11 Dec 2021 11:00:35: 6000000 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 @ Sat, 11 Dec 2021 11:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 11 Dec 2021 11:00:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:00:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:00:40: 7000000 INFO @ Sat, 11 Dec 2021 11:00:42: 1000000 INFO @ Sat, 11 Dec 2021 11:00:44: 8000000 INFO @ Sat, 11 Dec 2021 11:00:47: 2000000 INFO @ Sat, 11 Dec 2021 11:00:49: 9000000 INFO @ Sat, 11 Dec 2021 11:00:52: 3000000 INFO @ Sat, 11 Dec 2021 11:00:54: 10000000 INFO @ Sat, 11 Dec 2021 11:00:57: 4000000 INFO @ Sat, 11 Dec 2021 11:00:59: 11000000 INFO @ Sat, 11 Dec 2021 11:01:01: 5000000 INFO @ Sat, 11 Dec 2021 11:01:03: 12000000 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 @ Sat, 11 Dec 2021 11:01:06: 6000000 INFO @ Sat, 11 Dec 2021 11:01:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:01:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:01:06: #1 total tags in treatment: 12578813 INFO @ Sat, 11 Dec 2021 11:01:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:01:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:01:07: #1 tags after filtering in treatment: 12578813 INFO @ Sat, 11 Dec 2021 11:01:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:01:07: #1 finished! INFO @ Sat, 11 Dec 2021 11:01:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:01:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:01:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 11 Dec 2021 11:01:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:01:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:01:07: #2 number of paired peaks: 415 WARNING @ Sat, 11 Dec 2021 11:01:07: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sat, 11 Dec 2021 11:01:07: start model_add_line... INFO @ Sat, 11 Dec 2021 11:01:07: start X-correlation... INFO @ Sat, 11 Dec 2021 11:01:07: end of X-cor INFO @ Sat, 11 Dec 2021 11:01:07: #2 finished! INFO @ Sat, 11 Dec 2021 11:01:07: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 11:01:07: #2 alternative fragment length(s) may be 2,50,568 bps INFO @ Sat, 11 Dec 2021 11:01:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.05_model.r WARNING @ Sat, 11 Dec 2021 11:01:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:01:07: #2 You may need to consider one of the other alternative d(s): 2,50,568 WARNING @ Sat, 11 Dec 2021 11:01:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:01:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:01:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:01:11: 7000000 INFO @ Sat, 11 Dec 2021 11:01:13: 1000000 INFO @ Sat, 11 Dec 2021 11:01:16: 8000000 INFO @ Sat, 11 Dec 2021 11:01:19: 2000000 INFO @ Sat, 11 Dec 2021 11:01:21: 9000000 INFO @ Sat, 11 Dec 2021 11:01:25: 3000000 INFO @ Sat, 11 Dec 2021 11:01:26: 10000000 INFO @ Sat, 11 Dec 2021 11:01:30: 4000000 INFO @ Sat, 11 Dec 2021 11:01:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:01:31: 11000000 INFO @ Sat, 11 Dec 2021 11:01:36: 12000000 INFO @ Sat, 11 Dec 2021 11:01:36: 5000000 INFO @ Sat, 11 Dec 2021 11:01:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:01:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:01:38: #1 total tags in treatment: 12578813 INFO @ Sat, 11 Dec 2021 11:01:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:01:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:01:39: #1 tags after filtering in treatment: 12578813 INFO @ Sat, 11 Dec 2021 11:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:01:39: #1 finished! INFO @ Sat, 11 Dec 2021 11:01:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:01:39: #2 number of paired peaks: 415 WARNING @ Sat, 11 Dec 2021 11:01:39: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sat, 11 Dec 2021 11:01:39: start model_add_line... INFO @ Sat, 11 Dec 2021 11:01:40: start X-correlation... INFO @ Sat, 11 Dec 2021 11:01:40: end of X-cor INFO @ Sat, 11 Dec 2021 11:01:40: #2 finished! INFO @ Sat, 11 Dec 2021 11:01:40: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 11:01:40: #2 alternative fragment length(s) may be 2,50,568 bps INFO @ Sat, 11 Dec 2021 11:01:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.10_model.r WARNING @ Sat, 11 Dec 2021 11:01:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:01:40: #2 You may need to consider one of the other alternative d(s): 2,50,568 WARNING @ Sat, 11 Dec 2021 11:01:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:01:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:01:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:01:41: 6000000 INFO @ Sat, 11 Dec 2021 11:01:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:01:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:01:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.05_summits.bed INFO @ Sat, 11 Dec 2021 11:01:42: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2586 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:01:47: 7000000 INFO @ Sat, 11 Dec 2021 11:01:52: 8000000 INFO @ Sat, 11 Dec 2021 11:01:58: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:02:03: 10000000 INFO @ Sat, 11 Dec 2021 11:02:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:02:08: 11000000 INFO @ Sat, 11 Dec 2021 11:02:14: 12000000 INFO @ Sat, 11 Dec 2021 11:02:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:02:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:02:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.10_summits.bed INFO @ Sat, 11 Dec 2021 11:02:15: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1518 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:02:17: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:02:17: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:02:17: #1 total tags in treatment: 12578813 INFO @ Sat, 11 Dec 2021 11:02:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:02:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:02:17: #1 tags after filtering in treatment: 12578813 INFO @ Sat, 11 Dec 2021 11:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:02:17: #1 finished! INFO @ Sat, 11 Dec 2021 11:02:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:02:18: #2 number of paired peaks: 415 WARNING @ Sat, 11 Dec 2021 11:02:18: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sat, 11 Dec 2021 11:02:18: start model_add_line... INFO @ Sat, 11 Dec 2021 11:02:18: start X-correlation... INFO @ Sat, 11 Dec 2021 11:02:18: end of X-cor INFO @ Sat, 11 Dec 2021 11:02:18: #2 finished! INFO @ Sat, 11 Dec 2021 11:02:18: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 11:02:18: #2 alternative fragment length(s) may be 2,50,568 bps INFO @ Sat, 11 Dec 2021 11:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.20_model.r WARNING @ Sat, 11 Dec 2021 11:02:18: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:02:18: #2 You may need to consider one of the other alternative d(s): 2,50,568 WARNING @ Sat, 11 Dec 2021 11:02:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:02:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:02:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:02:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986133/SRX9986133.20_summits.bed INFO @ Sat, 11 Dec 2021 11:02:53: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (392 records, 4 fields): 2 millis CompletedMACS2peakCalling