Job ID = 6454210 SRX = SRX187589 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:22:15 prefetch.2.10.7: 1) Downloading 'SRR572653'... 2020-06-21T09:22:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:26:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:26:33 prefetch.2.10.7: 1) 'SRR572653' was downloaded successfully Read 38257052 spots for SRR572653/SRR572653.sra Written 38257052 spots for SRR572653/SRR572653.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: 00:06:13 38257052 reads; of these: 38257052 (100.00%) were unpaired; of these: 15458670 (40.41%) aligned 0 times 17626955 (46.08%) aligned exactly 1 time 5171427 (13.52%) aligned >1 times 59.59% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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 8 files... [bam_rmdupse_core] 14467897 / 22798382 = 0.6346 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 18:39:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.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 18:39:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:48: 1000000 INFO @ Sun, 21 Jun 2020 18:39:55: 2000000 INFO @ Sun, 21 Jun 2020 18:40:02: 3000000 INFO @ Sun, 21 Jun 2020 18:40:09: 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 @ Sun, 21 Jun 2020 18:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.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 18:40:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:16: 5000000 INFO @ Sun, 21 Jun 2020 18:40:19: 1000000 INFO @ Sun, 21 Jun 2020 18:40:23: 6000000 INFO @ Sun, 21 Jun 2020 18:40:26: 2000000 INFO @ Sun, 21 Jun 2020 18:40:31: 7000000 INFO @ Sun, 21 Jun 2020 18:40:33: 3000000 INFO @ Sun, 21 Jun 2020 18:40:38: 8000000 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 18:40:40: 4000000 INFO @ Sun, 21 Jun 2020 18:40:41: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:40:41: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:40:41: #1 total tags in treatment: 8330485 INFO @ Sun, 21 Jun 2020 18:40:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:41: #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 18:40:41: #1 tags after filtering in treatment: 8330477 INFO @ Sun, 21 Jun 2020 18:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.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 18:40:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:42: #2 number of paired peaks: 1206 INFO @ Sun, 21 Jun 2020 18:40:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:42: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 18:40:42: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 18:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.05_model.r WARNING @ Sun, 21 Jun 2020 18:40:42: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:40:42: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 18:40:42: #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 18:40:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:47: 5000000 INFO @ Sun, 21 Jun 2020 18:40:48: 1000000 INFO @ Sun, 21 Jun 2020 18:40:54: 6000000 INFO @ Sun, 21 Jun 2020 18:40:55: 2000000 INFO @ Sun, 21 Jun 2020 18:40:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:02: 3000000 INFO @ Sun, 21 Jun 2020 18:41:02: 7000000 INFO @ Sun, 21 Jun 2020 18:41:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.05_summits.bed INFO @ Sun, 21 Jun 2020 18:41:07: Done! pass1 - making usageList (637 chroms): 3 millis pass2 - checking and writing primary data (3108 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:41:08: 4000000 INFO @ Sun, 21 Jun 2020 18:41:09: 8000000 INFO @ Sun, 21 Jun 2020 18:41:11: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:41:11: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:41:11: #1 total tags in treatment: 8330485 INFO @ Sun, 21 Jun 2020 18:41:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:11: #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 18:41:12: #1 tags after filtering in treatment: 8330477 INFO @ Sun, 21 Jun 2020 18:41:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:13: #2 number of paired peaks: 1206 INFO @ Sun, 21 Jun 2020 18:41:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:13: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 18:41:13: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 18:41:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.10_model.r WARNING @ Sun, 21 Jun 2020 18:41:13: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:41:13: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 18:41:13: #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 18:41:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:14: 5000000 INFO @ Sun, 21 Jun 2020 18:41:20: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:41:27: 7000000 INFO @ Sun, 21 Jun 2020 18:41:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:33: 8000000 INFO @ Sun, 21 Jun 2020 18:41:36: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:41:36: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:41:36: #1 total tags in treatment: 8330485 INFO @ Sun, 21 Jun 2020 18:41:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:36: #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 18:41:36: #1 tags after filtering in treatment: 8330477 INFO @ Sun, 21 Jun 2020 18:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:37: #2 number of paired peaks: 1206 INFO @ Sun, 21 Jun 2020 18:41:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:37: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 18:41:37: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 18:41:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.20_model.r WARNING @ Sun, 21 Jun 2020 18:41:37: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:41:37: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 18:41:37: #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 18:41:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.10_summits.bed INFO @ Sun, 21 Jun 2020 18:41:38: Done! pass1 - making usageList (465 chroms): 1 millis pass2 - checking and writing primary data (2203 records, 4 fields): 29 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:41:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX187589/SRX187589.20_summits.bed INFO @ Sun, 21 Jun 2020 18:42:02: Done! pass1 - making usageList (360 chroms): 1 millis pass2 - checking and writing primary data (963 records, 4 fields): 22 millis CompletedMACS2peakCalling