Job ID = 6452929 SRX = SRX050596 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:52:00 prefetch.2.10.7: 1) Downloading 'SRR139078'... 2020-06-21T07:52:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:56:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:56:11 prefetch.2.10.7: 'SRR139078' is valid 2020-06-21T07:56:11 prefetch.2.10.7: 1) 'SRR139078' was downloaded successfully Read 27506893 spots for SRR139078/SRR139078.sra Written 27506893 spots for SRR139078/SRR139078.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: 00:06:17 27506893 reads; of these: 27506893 (100.00%) were unpaired; of these: 1363713 (4.96%) aligned 0 times 17651601 (64.17%) aligned exactly 1 time 8491579 (30.87%) aligned >1 times 95.04% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 11307614 / 26143180 = 0.4325 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 17:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.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 17:07:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:07:45: 1000000 INFO @ Sun, 21 Jun 2020 17:07:50: 2000000 INFO @ Sun, 21 Jun 2020 17:07:56: 3000000 INFO @ Sun, 21 Jun 2020 17:08:01: 4000000 INFO @ Sun, 21 Jun 2020 17:08:06: 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 17:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.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 17:08:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:11: 6000000 INFO @ Sun, 21 Jun 2020 17:08:15: 1000000 INFO @ Sun, 21 Jun 2020 17:08:16: 7000000 INFO @ Sun, 21 Jun 2020 17:08:20: 2000000 INFO @ Sun, 21 Jun 2020 17:08:22: 8000000 INFO @ Sun, 21 Jun 2020 17:08:26: 3000000 INFO @ Sun, 21 Jun 2020 17:08:27: 9000000 INFO @ Sun, 21 Jun 2020 17:08:31: 4000000 INFO @ Sun, 21 Jun 2020 17:08:32: 10000000 INFO @ Sun, 21 Jun 2020 17:08:36: 5000000 INFO @ Sun, 21 Jun 2020 17:08:37: 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 17:08:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.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 17:08:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:42: 6000000 INFO @ Sun, 21 Jun 2020 17:08:43: 12000000 INFO @ Sun, 21 Jun 2020 17:08:45: 1000000 INFO @ Sun, 21 Jun 2020 17:08:47: 7000000 INFO @ Sun, 21 Jun 2020 17:08:48: 13000000 INFO @ Sun, 21 Jun 2020 17:08:51: 2000000 INFO @ Sun, 21 Jun 2020 17:08:52: 8000000 INFO @ Sun, 21 Jun 2020 17:08:53: 14000000 INFO @ Sun, 21 Jun 2020 17:08:56: 3000000 INFO @ Sun, 21 Jun 2020 17:08:58: 9000000 INFO @ Sun, 21 Jun 2020 17:08:58: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:08:58: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:08:58: #1 total tags in treatment: 14835566 INFO @ Sun, 21 Jun 2020 17:08:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:08:58: #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 17:08:59: #1 tags after filtering in treatment: 14835514 INFO @ Sun, 21 Jun 2020 17:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:08:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:08:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:00: #2 number of paired peaks: 2792 INFO @ Sun, 21 Jun 2020 17:09:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:00: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:09:00: #2 alternative fragment length(s) may be 1,39 bps INFO @ Sun, 21 Jun 2020 17:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.05_model.r WARNING @ Sun, 21 Jun 2020 17:09:00: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:00: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Sun, 21 Jun 2020 17:09:00: #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 17:09:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:01: 4000000 INFO @ Sun, 21 Jun 2020 17:09:03: 10000000 INFO @ Sun, 21 Jun 2020 17:09:07: 5000000 INFO @ Sun, 21 Jun 2020 17:09:08: 11000000 INFO @ Sun, 21 Jun 2020 17:09:12: 6000000 INFO @ Sun, 21 Jun 2020 17:09:13: 12000000 INFO @ Sun, 21 Jun 2020 17:09:17: 7000000 INFO @ Sun, 21 Jun 2020 17:09:19: 13000000 INFO @ Sun, 21 Jun 2020 17:09:23: 8000000 INFO @ Sun, 21 Jun 2020 17:09:24: 14000000 INFO @ Sun, 21 Jun 2020 17:09:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:28: 9000000 INFO @ Sun, 21 Jun 2020 17:09:29: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:29: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:29: #1 total tags in treatment: 14835566 INFO @ Sun, 21 Jun 2020 17:09:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:29: #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 17:09:29: #1 tags after filtering in treatment: 14835514 INFO @ Sun, 21 Jun 2020 17:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:31: #2 number of paired peaks: 2792 INFO @ Sun, 21 Jun 2020 17:09:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:31: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:09:31: #2 alternative fragment length(s) may be 1,39 bps INFO @ Sun, 21 Jun 2020 17:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.10_model.r WARNING @ Sun, 21 Jun 2020 17:09:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:31: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Sun, 21 Jun 2020 17:09:31: #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 17:09:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:33: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.05_summits.bed INFO @ Sun, 21 Jun 2020 17:09:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:09:38: 11000000 INFO @ Sun, 21 Jun 2020 17:09:44: 12000000 INFO @ Sun, 21 Jun 2020 17:09:49: 13000000 INFO @ Sun, 21 Jun 2020 17:09:54: 14000000 INFO @ Sun, 21 Jun 2020 17:09:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:59: #1 total tags in treatment: 14835566 INFO @ Sun, 21 Jun 2020 17:09:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:59: #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 17:09:59: #1 tags after filtering in treatment: 14835514 INFO @ Sun, 21 Jun 2020 17:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:00: #2 number of paired peaks: 2792 INFO @ Sun, 21 Jun 2020 17:10:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:10:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:10:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:10:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:10:00: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:10:00: #2 alternative fragment length(s) may be 1,39 bps INFO @ Sun, 21 Jun 2020 17:10:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.20_model.r WARNING @ Sun, 21 Jun 2020 17:10:00: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:10:00: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Sun, 21 Jun 2020 17:10:00: #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 17:10:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:10:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.10_summits.bed INFO @ Sun, 21 Jun 2020 17:10:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:10:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050596/SRX050596.20_summits.bed INFO @ Sun, 21 Jun 2020 17:10:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling