Job ID = 6455295 SRX = SRX287672 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:25 prefetch.2.10.7: 1) Downloading 'SRR869860'... 2020-06-21T09:48:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:53 prefetch.2.10.7: 'SRR869860' is valid 2020-06-21T09:50:53 prefetch.2.10.7: 1) 'SRR869860' was downloaded successfully Read 14272941 spots for SRR869860/SRR869860.sra Written 14272941 spots for SRR869860/SRR869860.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: 00:07:45 14272941 reads; of these: 14272941 (100.00%) were unpaired; of these: 1182408 (8.28%) aligned 0 times 2288380 (16.03%) aligned exactly 1 time 10802153 (75.68%) aligned >1 times 91.72% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 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] 6823788 / 13090533 = 0.5213 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 19:02:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.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 19:02:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:22: 1000000 INFO @ Sun, 21 Jun 2020 19:02:28: 2000000 INFO @ Sun, 21 Jun 2020 19:02:33: 3000000 INFO @ Sun, 21 Jun 2020 19:02:38: 4000000 INFO @ Sun, 21 Jun 2020 19:02:43: 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 19:02:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.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 19:02:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:49: 6000000 INFO @ Sun, 21 Jun 2020 19:02:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:50: #1 total tags in treatment: 6266745 INFO @ Sun, 21 Jun 2020 19:02:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:50: #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 19:02:51: #1 tags after filtering in treatment: 6266742 INFO @ Sun, 21 Jun 2020 19:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:52: #2 number of paired peaks: 6798 INFO @ Sun, 21 Jun 2020 19:02:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:52: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 19:02:52: #2 alternative fragment length(s) may be 3,58 bps INFO @ Sun, 21 Jun 2020 19:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.05_model.r WARNING @ Sun, 21 Jun 2020 19:02:52: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:02:52: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Sun, 21 Jun 2020 19:02:52: #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 19:02:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:53: 1000000 INFO @ Sun, 21 Jun 2020 19:02:58: 2000000 INFO @ Sun, 21 Jun 2020 19:03:03: 3000000 INFO @ Sun, 21 Jun 2020 19:03:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:09: 4000000 INFO @ Sun, 21 Jun 2020 19:03:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.05_summits.bed INFO @ Sun, 21 Jun 2020 19:03:11: Done! pass1 - making usageList (1249 chroms): 2 millis pass2 - checking and writing primary data (5338 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:14: 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 19:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.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 19:03:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:20: 6000000 INFO @ Sun, 21 Jun 2020 19:03:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:21: #1 total tags in treatment: 6266745 INFO @ Sun, 21 Jun 2020 19:03:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:21: #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 19:03:22: #1 tags after filtering in treatment: 6266742 INFO @ Sun, 21 Jun 2020 19:03:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:23: #2 number of paired peaks: 6798 INFO @ Sun, 21 Jun 2020 19:03:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:23: 1000000 INFO @ Sun, 21 Jun 2020 19:03:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:23: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 19:03:23: #2 alternative fragment length(s) may be 3,58 bps INFO @ Sun, 21 Jun 2020 19:03:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.10_model.r WARNING @ Sun, 21 Jun 2020 19:03:23: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:03:23: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Sun, 21 Jun 2020 19:03:23: #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 19:03:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:28: 2000000 INFO @ Sun, 21 Jun 2020 19:03:34: 3000000 INFO @ Sun, 21 Jun 2020 19:03:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:39: 4000000 INFO @ Sun, 21 Jun 2020 19:03:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.10_summits.bed INFO @ Sun, 21 Jun 2020 19:03:41: Done! pass1 - making usageList (1022 chroms): 1 millis pass2 - checking and writing primary data (3606 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:44: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:03:50: 6000000 INFO @ Sun, 21 Jun 2020 19:03:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:51: #1 total tags in treatment: 6266745 INFO @ Sun, 21 Jun 2020 19:03:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:51: #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 19:03:52: #1 tags after filtering in treatment: 6266742 INFO @ Sun, 21 Jun 2020 19:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:53: #2 number of paired peaks: 6798 INFO @ Sun, 21 Jun 2020 19:03:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:53: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 19:03:53: #2 alternative fragment length(s) may be 3,58 bps INFO @ Sun, 21 Jun 2020 19:03:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.20_model.r WARNING @ Sun, 21 Jun 2020 19:03:53: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:03:53: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Sun, 21 Jun 2020 19:03:53: #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 19:03:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:04:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287672/SRX287672.20_summits.bed INFO @ Sun, 21 Jun 2020 19:04:12: Done! pass1 - making usageList (690 chroms): 1 millis pass2 - checking and writing primary data (1682 records, 4 fields): 18 millis CompletedMACS2peakCalling