Job ID = 6453391 SRX = SRX113318 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:24:02 prefetch.2.10.7: 1) Downloading 'SRR392930'... 2020-06-21T08:24:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:27:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:27:55 prefetch.2.10.7: 1) 'SRR392930' was downloaded successfully Read 20636266 spots for SRR392930/SRR392930.sra Written 20636266 spots for SRR392930/SRR392930.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: 00:05:25 20636266 reads; of these: 20636266 (100.00%) were unpaired; of these: 325739 (1.58%) aligned 0 times 14208395 (68.85%) aligned exactly 1 time 6102132 (29.57%) aligned >1 times 98.42% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 4637642 / 20310527 = 0.2283 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 17:39:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.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 17:39:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:17: 1000000 INFO @ Sun, 21 Jun 2020 17:39:21: 2000000 INFO @ Sun, 21 Jun 2020 17:39:26: 3000000 INFO @ Sun, 21 Jun 2020 17:39:31: 4000000 INFO @ Sun, 21 Jun 2020 17:39:36: 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 17:39:40: 6000000 INFO @ Sun, 21 Jun 2020 17:39:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.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 17:39:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:45: 7000000 INFO @ Sun, 21 Jun 2020 17:39:47: 1000000 INFO @ Sun, 21 Jun 2020 17:39:50: 8000000 INFO @ Sun, 21 Jun 2020 17:39:51: 2000000 INFO @ Sun, 21 Jun 2020 17:39:55: 9000000 INFO @ Sun, 21 Jun 2020 17:39:56: 3000000 INFO @ Sun, 21 Jun 2020 17:40:00: 10000000 INFO @ Sun, 21 Jun 2020 17:40:01: 4000000 INFO @ Sun, 21 Jun 2020 17:40:05: 11000000 INFO @ Sun, 21 Jun 2020 17:40:06: 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 17:40:10: 12000000 INFO @ Sun, 21 Jun 2020 17:40:11: 6000000 INFO @ Sun, 21 Jun 2020 17:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.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 17:40:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:40:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:40:15: 13000000 INFO @ Sun, 21 Jun 2020 17:40:16: 7000000 INFO @ Sun, 21 Jun 2020 17:40:17: 1000000 INFO @ Sun, 21 Jun 2020 17:40:21: 14000000 INFO @ Sun, 21 Jun 2020 17:40:21: 8000000 INFO @ Sun, 21 Jun 2020 17:40:22: 2000000 INFO @ Sun, 21 Jun 2020 17:40:26: 15000000 INFO @ Sun, 21 Jun 2020 17:40:26: 9000000 INFO @ Sun, 21 Jun 2020 17:40:27: 3000000 INFO @ Sun, 21 Jun 2020 17:40:29: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:40:29: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:40:29: #1 total tags in treatment: 15672885 INFO @ Sun, 21 Jun 2020 17:40:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:29: #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 17:40:30: #1 tags after filtering in treatment: 15672877 INFO @ Sun, 21 Jun 2020 17:40:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:30: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:31: #2 number of paired peaks: 306 WARNING @ Sun, 21 Jun 2020 17:40:31: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sun, 21 Jun 2020 17:40:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:31: 10000000 INFO @ Sun, 21 Jun 2020 17:40:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:31: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:40:31: #2 alternative fragment length(s) may be 2,12,35,38,68,460,515,518,539,569 bps INFO @ Sun, 21 Jun 2020 17:40:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.05_model.r WARNING @ Sun, 21 Jun 2020 17:40:31: #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 17:40:31: #2 You may need to consider one of the other alternative d(s): 2,12,35,38,68,460,515,518,539,569 WARNING @ Sun, 21 Jun 2020 17:40:31: #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 17:40:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:40:32: 4000000 INFO @ Sun, 21 Jun 2020 17:40:36: 11000000 INFO @ Sun, 21 Jun 2020 17:40:37: 5000000 INFO @ Sun, 21 Jun 2020 17:40:41: 12000000 INFO @ Sun, 21 Jun 2020 17:40:42: 6000000 INFO @ Sun, 21 Jun 2020 17:40:46: 13000000 INFO @ Sun, 21 Jun 2020 17:40:46: 7000000 INFO @ Sun, 21 Jun 2020 17:40:51: 14000000 INFO @ Sun, 21 Jun 2020 17:40:51: 8000000 INFO @ Sun, 21 Jun 2020 17:40:56: 15000000 INFO @ Sun, 21 Jun 2020 17:40:56: 9000000 INFO @ Sun, 21 Jun 2020 17:41:00: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:41:00: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:41:00: #1 total tags in treatment: 15672885 INFO @ Sun, 21 Jun 2020 17:41:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:41:00: #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 17:41:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:00: #1 tags after filtering in treatment: 15672877 INFO @ Sun, 21 Jun 2020 17:41:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:41:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:41:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:41:01: #2 number of paired peaks: 306 WARNING @ Sun, 21 Jun 2020 17:41:01: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sun, 21 Jun 2020 17:41:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:41:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:41:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:41:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:41:01: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:41:01: #2 alternative fragment length(s) may be 2,12,35,38,68,460,515,518,539,569 bps INFO @ Sun, 21 Jun 2020 17:41:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.10_model.r WARNING @ Sun, 21 Jun 2020 17:41:01: #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 17:41:01: #2 You may need to consider one of the other alternative d(s): 2,12,35,38,68,460,515,518,539,569 WARNING @ Sun, 21 Jun 2020 17:41:01: #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 17:41:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:41:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:41:01: 10000000 INFO @ Sun, 21 Jun 2020 17:41:06: 11000000 INFO @ Sun, 21 Jun 2020 17:41:11: 12000000 INFO @ Sun, 21 Jun 2020 17:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:41:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.05_summits.bed INFO @ Sun, 21 Jun 2020 17:41:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:41:16: 13000000 INFO @ Sun, 21 Jun 2020 17:41:21: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:41:26: 15000000 INFO @ Sun, 21 Jun 2020 17:41:30: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:41:30: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:41:30: #1 total tags in treatment: 15672885 INFO @ Sun, 21 Jun 2020 17:41:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:41:30: #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 17:41:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:30: #1 tags after filtering in treatment: 15672877 INFO @ Sun, 21 Jun 2020 17:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:41:30: #1 finished! INFO @ Sun, 21 Jun 2020 17:41:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:41:31: #2 number of paired peaks: 306 WARNING @ Sun, 21 Jun 2020 17:41:31: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sun, 21 Jun 2020 17:41:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:41:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:41:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:41:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:41:31: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:41:31: #2 alternative fragment length(s) may be 2,12,35,38,68,460,515,518,539,569 bps INFO @ Sun, 21 Jun 2020 17:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.20_model.r WARNING @ Sun, 21 Jun 2020 17:41:31: #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 17:41:31: #2 You may need to consider one of the other alternative d(s): 2,12,35,38,68,460,515,518,539,569 WARNING @ Sun, 21 Jun 2020 17:41:31: #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 17:41:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.10_summits.bed INFO @ Sun, 21 Jun 2020 17:41:44: 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 17:42:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:42:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:42:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:42:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113318/SRX113318.20_summits.bed INFO @ Sun, 21 Jun 2020 17:42:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling