Job ID = 6455162 SRX = SRX2804223 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:59:55 prefetch.2.10.7: 1) Downloading 'SRR5534651'... 2020-06-21T09:59:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:02:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:02:34 prefetch.2.10.7: 1) 'SRR5534651' was downloaded successfully 2020-06-21T10:02:34 prefetch.2.10.7: 'SRR5534651' has 0 unresolved dependencies Read 32781705 spots for SRR5534651/SRR5534651.sra Written 32781705 spots for SRR5534651/SRR5534651.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: 00:08:13 32781705 reads; of these: 32781705 (100.00%) were unpaired; of these: 9508519 (29.01%) aligned 0 times 16118592 (49.17%) aligned exactly 1 time 7154594 (21.82%) aligned >1 times 70.99% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 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 12 files... [bam_rmdupse_core] 4043267 / 23273186 = 0.1737 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 19:17:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.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 19:17:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:14: 1000000 INFO @ Sun, 21 Jun 2020 19:17:19: 2000000 INFO @ Sun, 21 Jun 2020 19:17:24: 3000000 INFO @ Sun, 21 Jun 2020 19:17:29: 4000000 INFO @ Sun, 21 Jun 2020 19:17:34: 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 19:17:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.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 19:17:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:39: 6000000 INFO @ Sun, 21 Jun 2020 19:17:44: 1000000 INFO @ Sun, 21 Jun 2020 19:17:45: 7000000 INFO @ Sun, 21 Jun 2020 19:17:50: 2000000 INFO @ Sun, 21 Jun 2020 19:17:50: 8000000 INFO @ Sun, 21 Jun 2020 19:17:55: 3000000 INFO @ Sun, 21 Jun 2020 19:17:56: 9000000 INFO @ Sun, 21 Jun 2020 19:18:01: 4000000 INFO @ Sun, 21 Jun 2020 19:18:01: 10000000 INFO @ Sun, 21 Jun 2020 19:18:07: 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 19:18:07: 11000000 INFO @ Sun, 21 Jun 2020 19:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.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 19:18:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:12: 6000000 INFO @ Sun, 21 Jun 2020 19:18:12: 12000000 INFO @ Sun, 21 Jun 2020 19:18:14: 1000000 INFO @ Sun, 21 Jun 2020 19:18:18: 7000000 INFO @ Sun, 21 Jun 2020 19:18:18: 13000000 INFO @ Sun, 21 Jun 2020 19:18:20: 2000000 INFO @ Sun, 21 Jun 2020 19:18:23: 14000000 INFO @ Sun, 21 Jun 2020 19:18:23: 8000000 INFO @ Sun, 21 Jun 2020 19:18:25: 3000000 INFO @ Sun, 21 Jun 2020 19:18:29: 15000000 INFO @ Sun, 21 Jun 2020 19:18:29: 9000000 INFO @ Sun, 21 Jun 2020 19:18:31: 4000000 INFO @ Sun, 21 Jun 2020 19:18:35: 16000000 INFO @ Sun, 21 Jun 2020 19:18:35: 10000000 INFO @ Sun, 21 Jun 2020 19:18:37: 5000000 INFO @ Sun, 21 Jun 2020 19:18:41: 17000000 INFO @ Sun, 21 Jun 2020 19:18:41: 11000000 INFO @ Sun, 21 Jun 2020 19:18:43: 6000000 INFO @ Sun, 21 Jun 2020 19:18:47: 18000000 INFO @ Sun, 21 Jun 2020 19:18:47: 12000000 INFO @ Sun, 21 Jun 2020 19:18:49: 7000000 INFO @ Sun, 21 Jun 2020 19:18:53: 19000000 INFO @ Sun, 21 Jun 2020 19:18:53: 13000000 INFO @ Sun, 21 Jun 2020 19:18:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:18:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:18:54: #1 total tags in treatment: 19229919 INFO @ Sun, 21 Jun 2020 19:18:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:54: #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 19:18:54: 8000000 INFO @ Sun, 21 Jun 2020 19:18:55: #1 tags after filtering in treatment: 19229919 INFO @ Sun, 21 Jun 2020 19:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:56: #2 number of paired peaks: 632 WARNING @ Sun, 21 Jun 2020 19:18:56: Fewer paired peaks (632) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 632 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:56: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 19:18:56: #2 alternative fragment length(s) may be 3,61,586 bps INFO @ Sun, 21 Jun 2020 19:18:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.05_model.r WARNING @ Sun, 21 Jun 2020 19:18:56: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:18:56: #2 You may need to consider one of the other alternative d(s): 3,61,586 WARNING @ Sun, 21 Jun 2020 19:18:56: #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 19:18:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:59: 14000000 INFO @ Sun, 21 Jun 2020 19:19:00: 9000000 INFO @ Sun, 21 Jun 2020 19:19:04: 15000000 INFO @ Sun, 21 Jun 2020 19:19:06: 10000000 INFO @ Sun, 21 Jun 2020 19:19:10: 16000000 INFO @ Sun, 21 Jun 2020 19:19:11: 11000000 INFO @ Sun, 21 Jun 2020 19:19:16: 17000000 INFO @ Sun, 21 Jun 2020 19:19:17: 12000000 INFO @ Sun, 21 Jun 2020 19:19:22: 18000000 INFO @ Sun, 21 Jun 2020 19:19:22: 13000000 INFO @ Sun, 21 Jun 2020 19:19:27: 19000000 INFO @ Sun, 21 Jun 2020 19:19:28: 14000000 INFO @ Sun, 21 Jun 2020 19:19:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:19:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:19:29: #1 total tags in treatment: 19229919 INFO @ Sun, 21 Jun 2020 19:19:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:29: #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 19:19:29: #1 tags after filtering in treatment: 19229919 INFO @ Sun, 21 Jun 2020 19:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:31: #2 number of paired peaks: 632 WARNING @ Sun, 21 Jun 2020 19:19:31: Fewer paired peaks (632) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 632 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:31: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 19:19:31: #2 alternative fragment length(s) may be 3,61,586 bps INFO @ Sun, 21 Jun 2020 19:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.10_model.r WARNING @ Sun, 21 Jun 2020 19:19:31: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:31: #2 You may need to consider one of the other alternative d(s): 3,61,586 WARNING @ Sun, 21 Jun 2020 19:19:31: #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 19:19:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:33: 15000000 INFO @ Sun, 21 Jun 2020 19:19:39: 16000000 INFO @ Sun, 21 Jun 2020 19:19:44: 17000000 INFO @ Sun, 21 Jun 2020 19:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.05_summits.bed INFO @ Sun, 21 Jun 2020 19:19:49: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (744 chroms): 1 millis pass2 - checking and writing primary data (3428 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:49: 18000000 INFO @ Sun, 21 Jun 2020 19:19:55: 19000000 INFO @ Sun, 21 Jun 2020 19:19:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:19:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:19:56: #1 total tags in treatment: 19229919 INFO @ Sun, 21 Jun 2020 19:19:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:56: #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 19:19:57: #1 tags after filtering in treatment: 19229919 INFO @ Sun, 21 Jun 2020 19:19:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:57: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:58: #2 number of paired peaks: 632 WARNING @ Sun, 21 Jun 2020 19:19:58: Fewer paired peaks (632) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 632 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:58: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:58: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:58: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 19:19:58: #2 alternative fragment length(s) may be 3,61,586 bps INFO @ Sun, 21 Jun 2020 19:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.20_model.r WARNING @ Sun, 21 Jun 2020 19:19:58: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:58: #2 You may need to consider one of the other alternative d(s): 3,61,586 WARNING @ Sun, 21 Jun 2020 19:19:58: #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 19:19:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:20:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.10_summits.bed INFO @ Sun, 21 Jun 2020 19:20:23: Done! pass1 - making usageList (651 chroms): 2 millis pass2 - checking and writing primary data (2489 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:20:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804223/SRX2804223.20_summits.bed INFO @ Sun, 21 Jun 2020 19:20:50: Done! pass1 - making usageList (475 chroms): 1 millis pass2 - checking and writing primary data (1276 records, 4 fields): 14 millis CompletedMACS2peakCalling