Job ID = 6455630 SRX = SRX287942 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:13:21 prefetch.2.10.7: 1) Downloading 'SRR870131'... 2020-06-21T10:13:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:15:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:15:44 prefetch.2.10.7: 1) 'SRR870131' was downloaded successfully Read 17639345 spots for SRR870131/SRR870131.sra Written 17639345 spots for SRR870131/SRR870131.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: 00:00:01 Multiseed full-index search: 00:05:43 17639345 reads; of these: 17639345 (100.00%) were unpaired; of these: 1423312 (8.07%) aligned 0 times 10544825 (59.78%) aligned exactly 1 time 5671208 (32.15%) aligned >1 times 91.93% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 3174744 / 16216033 = 0.1958 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 19:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.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 19:26:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:38: 1000000 INFO @ Sun, 21 Jun 2020 19:26:43: 2000000 INFO @ Sun, 21 Jun 2020 19:26:47: 3000000 INFO @ Sun, 21 Jun 2020 19:26:52: 4000000 INFO @ Sun, 21 Jun 2020 19:26:57: 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 19:27:02: 6000000 INFO @ Sun, 21 Jun 2020 19:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.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 19:27:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:07: 7000000 INFO @ Sun, 21 Jun 2020 19:27:08: 1000000 INFO @ Sun, 21 Jun 2020 19:27:12: 8000000 INFO @ Sun, 21 Jun 2020 19:27:13: 2000000 INFO @ Sun, 21 Jun 2020 19:27:17: 9000000 INFO @ Sun, 21 Jun 2020 19:27:18: 3000000 INFO @ Sun, 21 Jun 2020 19:27:22: 10000000 INFO @ Sun, 21 Jun 2020 19:27:23: 4000000 INFO @ Sun, 21 Jun 2020 19:27:27: 11000000 INFO @ Sun, 21 Jun 2020 19:27:28: 5000000 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 19:27:32: 12000000 INFO @ Sun, 21 Jun 2020 19:27:33: 6000000 INFO @ Sun, 21 Jun 2020 19:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.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 19:27:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:37: 13000000 INFO @ Sun, 21 Jun 2020 19:27:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:37: #1 total tags in treatment: 13041289 INFO @ Sun, 21 Jun 2020 19:27:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:37: #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 19:27:38: #1 tags after filtering in treatment: 13041289 INFO @ Sun, 21 Jun 2020 19:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:38: 7000000 INFO @ Sun, 21 Jun 2020 19:27:38: #2 number of paired peaks: 673 WARNING @ Sun, 21 Jun 2020 19:27:38: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:39: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:27:39: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.05_model.r WARNING @ Sun, 21 Jun 2020 19:27:39: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:39: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:27:39: #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 19:27:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:39: 1000000 INFO @ Sun, 21 Jun 2020 19:27:43: 8000000 INFO @ Sun, 21 Jun 2020 19:27:44: 2000000 INFO @ Sun, 21 Jun 2020 19:27:48: 9000000 INFO @ Sun, 21 Jun 2020 19:27:49: 3000000 INFO @ Sun, 21 Jun 2020 19:27:53: 10000000 INFO @ Sun, 21 Jun 2020 19:27:54: 4000000 INFO @ Sun, 21 Jun 2020 19:27:58: 11000000 INFO @ Sun, 21 Jun 2020 19:27:59: 5000000 INFO @ Sun, 21 Jun 2020 19:28:03: 12000000 INFO @ Sun, 21 Jun 2020 19:28:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:05: 6000000 INFO @ Sun, 21 Jun 2020 19:28:08: 13000000 INFO @ Sun, 21 Jun 2020 19:28:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:08: #1 total tags in treatment: 13041289 INFO @ Sun, 21 Jun 2020 19:28:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:08: #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 19:28:09: #1 tags after filtering in treatment: 13041289 INFO @ Sun, 21 Jun 2020 19:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:10: 7000000 INFO @ Sun, 21 Jun 2020 19:28:10: #2 number of paired peaks: 673 WARNING @ Sun, 21 Jun 2020 19:28:10: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Sun, 21 Jun 2020 19:28:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:10: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:28:10: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:28:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.10_model.r WARNING @ Sun, 21 Jun 2020 19:28:10: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:10: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:28:10: #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 19:28:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:15: 8000000 INFO @ Sun, 21 Jun 2020 19:28:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.05_summits.bed INFO @ Sun, 21 Jun 2020 19:28:15: Done! pass1 - making usageList (637 chroms): 1 millis pass2 - checking and writing primary data (2525 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:20: 9000000 INFO @ Sun, 21 Jun 2020 19:28:24: 10000000 INFO @ Sun, 21 Jun 2020 19:28:30: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:28:35: 12000000 INFO @ Sun, 21 Jun 2020 19:28:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:40: 13000000 INFO @ Sun, 21 Jun 2020 19:28:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:40: #1 total tags in treatment: 13041289 INFO @ Sun, 21 Jun 2020 19:28:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:40: #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 19:28:40: #1 tags after filtering in treatment: 13041289 INFO @ Sun, 21 Jun 2020 19:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:41: #2 number of paired peaks: 673 WARNING @ Sun, 21 Jun 2020 19:28:41: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Sun, 21 Jun 2020 19:28:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:41: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:28:41: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:28:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.20_model.r WARNING @ Sun, 21 Jun 2020 19:28:41: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:41: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:28:41: #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 19:28:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.10_summits.bed INFO @ Sun, 21 Jun 2020 19:28:47: Done! pass1 - making usageList (533 chroms): 1 millis pass2 - checking and writing primary data (2003 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:29:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287942/SRX287942.20_summits.bed INFO @ Sun, 21 Jun 2020 19:29:17: Done! pass1 - making usageList (324 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 9 millis CompletedMACS2peakCalling