Job ID = 6455274 SRX = SRX287654 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:55 prefetch.2.10.7: 1) Downloading 'SRR869841'... 2020-06-21T09:53:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:57:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:57:36 prefetch.2.10.7: 1) 'SRR869841' was downloaded successfully Read 18022423 spots for SRR869841/SRR869841.sra Written 18022423 spots for SRR869841/SRR869841.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: 00:04:51 18022423 reads; of these: 18022423 (100.00%) were unpaired; of these: 1505229 (8.35%) aligned 0 times 12417472 (68.90%) aligned exactly 1 time 4099722 (22.75%) aligned >1 times 91.65% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2374673 / 16517194 = 0.1438 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 @ Sun, 21 Jun 2020 19:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.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 @ Sun, 21 Jun 2020 19:08:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:05: 1000000 INFO @ Sun, 21 Jun 2020 19:08:10: 2000000 INFO @ Sun, 21 Jun 2020 19:08:15: 3000000 INFO @ Sun, 21 Jun 2020 19:08:21: 4000000 INFO @ Sun, 21 Jun 2020 19:08:26: 5000000 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 @ Sun, 21 Jun 2020 19:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.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 @ Sun, 21 Jun 2020 19:08:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:31: 6000000 INFO @ Sun, 21 Jun 2020 19:08:35: 1000000 INFO @ Sun, 21 Jun 2020 19:08:36: 7000000 INFO @ Sun, 21 Jun 2020 19:08:41: 2000000 INFO @ Sun, 21 Jun 2020 19:08:41: 8000000 INFO @ Sun, 21 Jun 2020 19:08:46: 3000000 INFO @ Sun, 21 Jun 2020 19:08:46: 9000000 INFO @ Sun, 21 Jun 2020 19:08:51: 4000000 INFO @ Sun, 21 Jun 2020 19:08:51: 10000000 INFO @ Sun, 21 Jun 2020 19:08:56: 5000000 INFO @ Sun, 21 Jun 2020 19:08:57: 11000000 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 @ Sun, 21 Jun 2020 19:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.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 @ Sun, 21 Jun 2020 19:09:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:02: 6000000 INFO @ Sun, 21 Jun 2020 19:09:02: 12000000 INFO @ Sun, 21 Jun 2020 19:09:06: 1000000 INFO @ Sun, 21 Jun 2020 19:09:07: 7000000 INFO @ Sun, 21 Jun 2020 19:09:08: 13000000 INFO @ Sun, 21 Jun 2020 19:09:11: 2000000 INFO @ Sun, 21 Jun 2020 19:09:12: 8000000 INFO @ Sun, 21 Jun 2020 19:09:13: 14000000 INFO @ Sun, 21 Jun 2020 19:09:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:14: #1 total tags in treatment: 14142521 INFO @ Sun, 21 Jun 2020 19:09:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:09:14: #1 tags after filtering in treatment: 14142521 INFO @ Sun, 21 Jun 2020 19:09:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:15: #2 number of paired peaks: 335 WARNING @ Sun, 21 Jun 2020 19:09:15: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 21 Jun 2020 19:09:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:16: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:09:16: #2 alternative fragment length(s) may be 4,41 bps INFO @ Sun, 21 Jun 2020 19:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.05_model.r WARNING @ Sun, 21 Jun 2020 19:09:16: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:16: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Sun, 21 Jun 2020 19:09:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:09:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:17: 3000000 INFO @ Sun, 21 Jun 2020 19:09:18: 9000000 INFO @ Sun, 21 Jun 2020 19:09:22: 4000000 INFO @ Sun, 21 Jun 2020 19:09:23: 10000000 INFO @ Sun, 21 Jun 2020 19:09:28: 5000000 INFO @ Sun, 21 Jun 2020 19:09:28: 11000000 INFO @ Sun, 21 Jun 2020 19:09:33: 6000000 INFO @ Sun, 21 Jun 2020 19:09:34: 12000000 INFO @ Sun, 21 Jun 2020 19:09:38: 7000000 INFO @ Sun, 21 Jun 2020 19:09:39: 13000000 INFO @ Sun, 21 Jun 2020 19:09:44: 8000000 INFO @ Sun, 21 Jun 2020 19:09:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:45: 14000000 INFO @ Sun, 21 Jun 2020 19:09:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:45: #1 total tags in treatment: 14142521 INFO @ Sun, 21 Jun 2020 19:09:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:09:46: #1 tags after filtering in treatment: 14142521 INFO @ Sun, 21 Jun 2020 19:09:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:47: #2 number of paired peaks: 335 WARNING @ Sun, 21 Jun 2020 19:09:47: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 21 Jun 2020 19:09:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:47: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:09:47: #2 alternative fragment length(s) may be 4,41 bps INFO @ Sun, 21 Jun 2020 19:09:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.10_model.r WARNING @ Sun, 21 Jun 2020 19:09:47: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:47: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Sun, 21 Jun 2020 19:09:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:09:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:49: 9000000 INFO @ Sun, 21 Jun 2020 19:09:54: 10000000 INFO @ Sun, 21 Jun 2020 19:09:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.05_summits.bed INFO @ Sun, 21 Jun 2020 19:09:57: Done! pass1 - making usageList (559 chroms): 1 millis pass2 - checking and writing primary data (2323 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:59: 11000000 INFO @ Sun, 21 Jun 2020 19:10:04: 12000000 INFO @ Sun, 21 Jun 2020 19:10:09: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:10:14: 14000000 INFO @ Sun, 21 Jun 2020 19:10:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:15: #1 total tags in treatment: 14142521 INFO @ Sun, 21 Jun 2020 19:10:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:10:16: #1 tags after filtering in treatment: 14142521 INFO @ Sun, 21 Jun 2020 19:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:17: #2 number of paired peaks: 335 WARNING @ Sun, 21 Jun 2020 19:10:17: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:17: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:10:17: #2 alternative fragment length(s) may be 4,41 bps INFO @ Sun, 21 Jun 2020 19:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.20_model.r WARNING @ Sun, 21 Jun 2020 19:10:17: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:17: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Sun, 21 Jun 2020 19:10:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:10:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.10_summits.bed INFO @ Sun, 21 Jun 2020 19:10:29: Done! pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (1363 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287654/SRX287654.20_summits.bed INFO @ Sun, 21 Jun 2020 19:10:57: Done! pass1 - making usageList (225 chroms): 1 millis pass2 - checking and writing primary data (464 records, 4 fields): 22 millis CompletedMACS2peakCalling