Job ID = 6498421 SRX = SRX495278 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:25:16 prefetch.2.10.7: 1) Downloading 'SRR1198783'... 2020-06-25T23:25:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:28:20 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:28:20 prefetch.2.10.7: 1) 'SRR1198783' was downloaded successfully Read 24529628 spots for SRR1198783/SRR1198783.sra Written 24529628 spots for SRR1198783/SRR1198783.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: 00:10:39 24529628 reads; of these: 24529628 (100.00%) were unpaired; of these: 4027424 (16.42%) aligned 0 times 10529748 (42.93%) aligned exactly 1 time 9972456 (40.65%) aligned >1 times 83.58% overall alignment rate Time searching: 00:10:39 Overall time: 00:10:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 8295069 / 20502204 = 0.4046 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 @ Fri, 26 Jun 2020 08:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.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 @ Fri, 26 Jun 2020 08:44:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:44:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:45:00: 1000000 INFO @ Fri, 26 Jun 2020 08:45:06: 2000000 INFO @ Fri, 26 Jun 2020 08:45:12: 3000000 INFO @ Fri, 26 Jun 2020 08:45:19: 4000000 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 @ Fri, 26 Jun 2020 08:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.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 @ Fri, 26 Jun 2020 08:45:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:45:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:45:25: 5000000 INFO @ Fri, 26 Jun 2020 08:45:29: 1000000 INFO @ Fri, 26 Jun 2020 08:45:32: 6000000 INFO @ Fri, 26 Jun 2020 08:45:35: 2000000 INFO @ Fri, 26 Jun 2020 08:45:38: 7000000 INFO @ Fri, 26 Jun 2020 08:45:41: 3000000 INFO @ Fri, 26 Jun 2020 08:45:45: 8000000 INFO @ Fri, 26 Jun 2020 08:45:47: 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 @ Fri, 26 Jun 2020 08:45:52: 9000000 INFO @ Fri, 26 Jun 2020 08:45:53: 5000000 INFO @ Fri, 26 Jun 2020 08:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.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 @ Fri, 26 Jun 2020 08:45:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:45:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:45:58: 10000000 INFO @ Fri, 26 Jun 2020 08:45:59: 6000000 INFO @ Fri, 26 Jun 2020 08:45:59: 1000000 INFO @ Fri, 26 Jun 2020 08:46:04: 7000000 INFO @ Fri, 26 Jun 2020 08:46:05: 11000000 INFO @ Fri, 26 Jun 2020 08:46:05: 2000000 INFO @ Fri, 26 Jun 2020 08:46:10: 8000000 INFO @ Fri, 26 Jun 2020 08:46:11: 3000000 INFO @ Fri, 26 Jun 2020 08:46:12: 12000000 INFO @ Fri, 26 Jun 2020 08:46:13: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:46:13: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:46:13: #1 total tags in treatment: 12207135 INFO @ Fri, 26 Jun 2020 08:46:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:46:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:46:14: #1 tags after filtering in treatment: 12207135 INFO @ Fri, 26 Jun 2020 08:46:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:46:14: #1 finished! INFO @ Fri, 26 Jun 2020 08:46:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:46:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:46:15: #2 number of paired peaks: 1727 INFO @ Fri, 26 Jun 2020 08:46:15: start model_add_line... INFO @ Fri, 26 Jun 2020 08:46:15: start X-correlation... INFO @ Fri, 26 Jun 2020 08:46:15: end of X-cor INFO @ Fri, 26 Jun 2020 08:46:15: #2 finished! INFO @ Fri, 26 Jun 2020 08:46:15: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 08:46:15: #2 alternative fragment length(s) may be 2,14 bps INFO @ Fri, 26 Jun 2020 08:46:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.05_model.r WARNING @ Fri, 26 Jun 2020 08:46:15: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:46:15: #2 You may need to consider one of the other alternative d(s): 2,14 WARNING @ Fri, 26 Jun 2020 08:46:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:46:15: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:46:16: 9000000 INFO @ Fri, 26 Jun 2020 08:46:17: 4000000 INFO @ Fri, 26 Jun 2020 08:46:22: 10000000 INFO @ Fri, 26 Jun 2020 08:46:23: 5000000 INFO @ Fri, 26 Jun 2020 08:46:27: 11000000 INFO @ Fri, 26 Jun 2020 08:46:28: 6000000 INFO @ Fri, 26 Jun 2020 08:46:33: 12000000 INFO @ Fri, 26 Jun 2020 08:46:34: 7000000 INFO @ Fri, 26 Jun 2020 08:46:35: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:46:35: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:46:35: #1 total tags in treatment: 12207135 INFO @ Fri, 26 Jun 2020 08:46:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:46:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:46:35: #1 tags after filtering in treatment: 12207135 INFO @ Fri, 26 Jun 2020 08:46:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:46:35: #1 finished! INFO @ Fri, 26 Jun 2020 08:46:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:46:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:46:36: #2 number of paired peaks: 1727 INFO @ Fri, 26 Jun 2020 08:46:36: start model_add_line... INFO @ Fri, 26 Jun 2020 08:46:36: start X-correlation... INFO @ Fri, 26 Jun 2020 08:46:36: end of X-cor INFO @ Fri, 26 Jun 2020 08:46:36: #2 finished! INFO @ Fri, 26 Jun 2020 08:46:36: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 08:46:36: #2 alternative fragment length(s) may be 2,14 bps INFO @ Fri, 26 Jun 2020 08:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.10_model.r WARNING @ Fri, 26 Jun 2020 08:46:36: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:46:36: #2 You may need to consider one of the other alternative d(s): 2,14 WARNING @ Fri, 26 Jun 2020 08:46:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:46:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:46:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:46:40: 8000000 INFO @ Fri, 26 Jun 2020 08:46:45: 9000000 INFO @ Fri, 26 Jun 2020 08:46:50: 10000000 INFO @ Fri, 26 Jun 2020 08:46:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:46:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:46:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.05_summits.bed INFO @ Fri, 26 Jun 2020 08:46:51: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:46:55: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:47:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:47:01: 12000000 INFO @ Fri, 26 Jun 2020 08:47:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:47:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:47:02: #1 total tags in treatment: 12207135 INFO @ Fri, 26 Jun 2020 08:47:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:47:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:47:02: #1 tags after filtering in treatment: 12207135 INFO @ Fri, 26 Jun 2020 08:47:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:47:02: #1 finished! INFO @ Fri, 26 Jun 2020 08:47:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:47:03: #2 number of paired peaks: 1727 INFO @ Fri, 26 Jun 2020 08:47:03: start model_add_line... INFO @ Fri, 26 Jun 2020 08:47:03: start X-correlation... INFO @ Fri, 26 Jun 2020 08:47:03: end of X-cor INFO @ Fri, 26 Jun 2020 08:47:03: #2 finished! INFO @ Fri, 26 Jun 2020 08:47:03: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 08:47:03: #2 alternative fragment length(s) may be 2,14 bps INFO @ Fri, 26 Jun 2020 08:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.20_model.r WARNING @ Fri, 26 Jun 2020 08:47:03: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:47:03: #2 You may need to consider one of the other alternative d(s): 2,14 WARNING @ Fri, 26 Jun 2020 08:47:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:47:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:47:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:47:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:47:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:47:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.10_summits.bed INFO @ Fri, 26 Jun 2020 08:47:12: 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 @ Fri, 26 Jun 2020 08:47:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:47:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:47:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:47:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495278/SRX495278.20_summits.bed INFO @ Fri, 26 Jun 2020 08:47:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling