Job ID = 6458141 SRX = SRX495258 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:16:36 prefetch.2.10.7: 1) Downloading 'SRR1198763'... 2020-06-21T12:16:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:18:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:18:24 prefetch.2.10.7: 1) 'SRR1198763' was downloaded successfully Read 22003233 spots for SRR1198763/SRR1198763.sra Written 22003233 spots for SRR1198763/SRR1198763.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: 00:04:27 22003233 reads; of these: 22003233 (100.00%) were unpaired; of these: 440967 (2.00%) aligned 0 times 18976536 (86.24%) aligned exactly 1 time 2585730 (11.75%) aligned >1 times 98.00% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 9473727 / 21562266 = 0.4394 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 21:28:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.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 21:28:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:26: 1000000 INFO @ Sun, 21 Jun 2020 21:28:31: 2000000 INFO @ Sun, 21 Jun 2020 21:28:37: 3000000 INFO @ Sun, 21 Jun 2020 21:28:42: 4000000 INFO @ Sun, 21 Jun 2020 21:28:48: 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 21:28:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.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 21:28:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:54: 6000000 INFO @ Sun, 21 Jun 2020 21:28:57: 1000000 INFO @ Sun, 21 Jun 2020 21:29:00: 7000000 INFO @ Sun, 21 Jun 2020 21:29:03: 2000000 INFO @ Sun, 21 Jun 2020 21:29:06: 8000000 INFO @ Sun, 21 Jun 2020 21:29:09: 3000000 INFO @ Sun, 21 Jun 2020 21:29:12: 9000000 INFO @ Sun, 21 Jun 2020 21:29:16: 4000000 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 21:29:19: 10000000 INFO @ Sun, 21 Jun 2020 21:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.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 21:29:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:22: 5000000 INFO @ Sun, 21 Jun 2020 21:29:25: 11000000 INFO @ Sun, 21 Jun 2020 21:29:26: 1000000 INFO @ Sun, 21 Jun 2020 21:29:28: 6000000 INFO @ Sun, 21 Jun 2020 21:29:32: 12000000 INFO @ Sun, 21 Jun 2020 21:29:33: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:29:33: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:29:33: #1 total tags in treatment: 12088539 INFO @ Sun, 21 Jun 2020 21:29:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:33: #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 21:29:33: 2000000 INFO @ Sun, 21 Jun 2020 21:29:33: #1 tags after filtering in treatment: 12088521 INFO @ Sun, 21 Jun 2020 21:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:34: #2 number of paired peaks: 3211 INFO @ Sun, 21 Jun 2020 21:29:34: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:34: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:34: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:34: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:34: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:29:34: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 21:29:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.05_model.r WARNING @ Sun, 21 Jun 2020 21:29:34: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:34: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 21:29:34: #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 21:29:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:35: 7000000 INFO @ Sun, 21 Jun 2020 21:29:39: 3000000 INFO @ Sun, 21 Jun 2020 21:29:41: 8000000 INFO @ Sun, 21 Jun 2020 21:29:46: 4000000 INFO @ Sun, 21 Jun 2020 21:29:48: 9000000 INFO @ Sun, 21 Jun 2020 21:29:52: 5000000 INFO @ Sun, 21 Jun 2020 21:29:54: 10000000 INFO @ Sun, 21 Jun 2020 21:29:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:59: 6000000 INFO @ Sun, 21 Jun 2020 21:30:01: 11000000 INFO @ Sun, 21 Jun 2020 21:30:05: 7000000 INFO @ Sun, 21 Jun 2020 21:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.05_summits.bed INFO @ Sun, 21 Jun 2020 21:30:07: Done! INFO @ Sun, 21 Jun 2020 21:30:08: 12000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:08: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:30:08: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:30:08: #1 total tags in treatment: 12088539 INFO @ Sun, 21 Jun 2020 21:30:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:08: #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 21:30:09: #1 tags after filtering in treatment: 12088521 INFO @ Sun, 21 Jun 2020 21:30:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:10: #2 number of paired peaks: 3211 INFO @ Sun, 21 Jun 2020 21:30:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:10: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:30:10: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 21:30:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.10_model.r WARNING @ Sun, 21 Jun 2020 21:30:10: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:10: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 21:30:10: #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 21:30:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:12: 8000000 INFO @ Sun, 21 Jun 2020 21:30:18: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:30:24: 10000000 INFO @ Sun, 21 Jun 2020 21:30:30: 11000000 INFO @ Sun, 21 Jun 2020 21:30:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:36: 12000000 INFO @ Sun, 21 Jun 2020 21:30:37: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:30:37: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:30:37: #1 total tags in treatment: 12088539 INFO @ Sun, 21 Jun 2020 21:30:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:37: #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 21:30:37: #1 tags after filtering in treatment: 12088521 INFO @ Sun, 21 Jun 2020 21:30:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:38: #2 number of paired peaks: 3211 INFO @ Sun, 21 Jun 2020 21:30:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:38: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:30:38: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 21:30:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.20_model.r WARNING @ Sun, 21 Jun 2020 21:30:38: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:38: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 21:30:38: #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 21:30:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.10_summits.bed INFO @ Sun, 21 Jun 2020 21:30:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:31:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495258/SRX495258.20_summits.bed INFO @ Sun, 21 Jun 2020 21:31:12: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling