Job ID = 6509220 SRX = SRX750071 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:15:28 prefetch.2.10.7: 1) Downloading 'SRR1638754'... 2020-06-26T15:15:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:19:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:19:34 prefetch.2.10.7: 1) 'SRR1638754' was downloaded successfully Read 37029482 spots for SRR1638754/SRR1638754.sra Written 37029482 spots for SRR1638754/SRR1638754.sra 2020-06-26T15:21:58 prefetch.2.10.7: 1) Downloading 'SRR1638755'... 2020-06-26T15:21:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:24:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:24:34 prefetch.2.10.7: 1) 'SRR1638755' was downloaded successfully Read 21812756 spots for SRR1638755/SRR1638755.sra Written 21812756 spots for SRR1638755/SRR1638755.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: 00:17:42 58842238 reads; of these: 58842238 (100.00%) were unpaired; of these: 3504317 (5.96%) aligned 0 times 43900045 (74.61%) aligned exactly 1 time 11437876 (19.44%) aligned >1 times 94.04% overall alignment rate Time searching: 00:17:42 Overall time: 00:17:42 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 24 files... [bam_rmdupse_core] 46359969 / 55337921 = 0.8378 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 @ Sat, 27 Jun 2020 00:53:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.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 @ Sat, 27 Jun 2020 00:53:15: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:53:15: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:53:21: 1000000 INFO @ Sat, 27 Jun 2020 00:53:26: 2000000 INFO @ Sat, 27 Jun 2020 00:53:32: 3000000 INFO @ Sat, 27 Jun 2020 00:53:38: 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 @ Sat, 27 Jun 2020 00:53:44: 5000000 INFO @ Sat, 27 Jun 2020 00:53:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.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 @ Sat, 27 Jun 2020 00:53:45: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:53:45: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:53:50: 6000000 INFO @ Sat, 27 Jun 2020 00:53:51: 1000000 INFO @ Sat, 27 Jun 2020 00:53:56: 7000000 INFO @ Sat, 27 Jun 2020 00:53:58: 2000000 INFO @ Sat, 27 Jun 2020 00:54:03: 8000000 INFO @ Sat, 27 Jun 2020 00:54:04: 3000000 INFO @ Sat, 27 Jun 2020 00:54:10: #1 tag size is determined as 67 bps INFO @ Sat, 27 Jun 2020 00:54:10: #1 tag size = 67 INFO @ Sat, 27 Jun 2020 00:54:10: #1 total tags in treatment: 8977952 INFO @ Sat, 27 Jun 2020 00:54:10: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:54:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:54:10: #1 tags after filtering in treatment: 8977934 INFO @ Sat, 27 Jun 2020 00:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:54:10: #1 finished! INFO @ Sat, 27 Jun 2020 00:54:10: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:54:10: 4000000 INFO @ Sat, 27 Jun 2020 00:54:11: #2 number of paired peaks: 6917 INFO @ Sat, 27 Jun 2020 00:54:11: start model_add_line... INFO @ Sat, 27 Jun 2020 00:54:11: start X-correlation... INFO @ Sat, 27 Jun 2020 00:54:11: end of X-cor INFO @ Sat, 27 Jun 2020 00:54:11: #2 finished! INFO @ Sat, 27 Jun 2020 00:54:11: #2 predicted fragment length is 131 bps INFO @ Sat, 27 Jun 2020 00:54:11: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 27 Jun 2020 00:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.05_model.r WARNING @ Sat, 27 Jun 2020 00:54:11: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:54:11: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Sat, 27 Jun 2020 00:54:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:54:11: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:54:11: #3 Pre-compute pvalue-qvalue table... 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 @ Sat, 27 Jun 2020 00:54:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.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 @ Sat, 27 Jun 2020 00:54:15: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:54:15: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:54:16: 5000000 INFO @ Sat, 27 Jun 2020 00:54:22: 1000000 INFO @ Sat, 27 Jun 2020 00:54:23: 6000000 INFO @ Sat, 27 Jun 2020 00:54:28: 2000000 INFO @ Sat, 27 Jun 2020 00:54:30: 7000000 INFO @ Sat, 27 Jun 2020 00:54:35: 3000000 INFO @ Sat, 27 Jun 2020 00:54:37: 8000000 INFO @ Sat, 27 Jun 2020 00:54:38: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:54:42: 4000000 INFO @ Sat, 27 Jun 2020 00:54:43: #1 tag size is determined as 67 bps INFO @ Sat, 27 Jun 2020 00:54:43: #1 tag size = 67 INFO @ Sat, 27 Jun 2020 00:54:43: #1 total tags in treatment: 8977952 INFO @ Sat, 27 Jun 2020 00:54:43: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:54:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:54:44: #1 tags after filtering in treatment: 8977934 INFO @ Sat, 27 Jun 2020 00:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:54:44: #1 finished! INFO @ Sat, 27 Jun 2020 00:54:44: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:54:45: #2 number of paired peaks: 6917 INFO @ Sat, 27 Jun 2020 00:54:45: start model_add_line... INFO @ Sat, 27 Jun 2020 00:54:45: start X-correlation... INFO @ Sat, 27 Jun 2020 00:54:45: end of X-cor INFO @ Sat, 27 Jun 2020 00:54:45: #2 finished! INFO @ Sat, 27 Jun 2020 00:54:45: #2 predicted fragment length is 131 bps INFO @ Sat, 27 Jun 2020 00:54:45: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 27 Jun 2020 00:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.10_model.r WARNING @ Sat, 27 Jun 2020 00:54:45: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:54:45: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Sat, 27 Jun 2020 00:54:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:54:45: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:54:48: 5000000 INFO @ Sat, 27 Jun 2020 00:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.05_summits.bed INFO @ Sat, 27 Jun 2020 00:54:49: Done! pass1 - making usageList (678 chroms): 2 millis pass2 - checking and writing primary data (8354 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:54:54: 6000000 INFO @ Sat, 27 Jun 2020 00:55:00: 7000000 INFO @ Sat, 27 Jun 2020 00:55:06: 8000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:55:12: #1 tag size is determined as 67 bps INFO @ Sat, 27 Jun 2020 00:55:12: #1 tag size = 67 INFO @ Sat, 27 Jun 2020 00:55:12: #1 total tags in treatment: 8977952 INFO @ Sat, 27 Jun 2020 00:55:12: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:55:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:55:13: #1 tags after filtering in treatment: 8977934 INFO @ Sat, 27 Jun 2020 00:55:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:55:13: #1 finished! INFO @ Sat, 27 Jun 2020 00:55:13: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:55:13: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:55:14: #2 number of paired peaks: 6917 INFO @ Sat, 27 Jun 2020 00:55:14: start model_add_line... INFO @ Sat, 27 Jun 2020 00:55:14: start X-correlation... INFO @ Sat, 27 Jun 2020 00:55:14: end of X-cor INFO @ Sat, 27 Jun 2020 00:55:14: #2 finished! INFO @ Sat, 27 Jun 2020 00:55:14: #2 predicted fragment length is 131 bps INFO @ Sat, 27 Jun 2020 00:55:14: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 27 Jun 2020 00:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.20_model.r WARNING @ Sat, 27 Jun 2020 00:55:14: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:55:14: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Sat, 27 Jun 2020 00:55:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:55:14: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:55:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.10_summits.bed INFO @ Sat, 27 Jun 2020 00:55:24: Done! pass1 - making usageList (515 chroms): 1 millis pass2 - checking and writing primary data (5799 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:55:41: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:55:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:55:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:55:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750071/SRX750071.20_summits.bed INFO @ Sat, 27 Jun 2020 00:55:52: Done! pass1 - making usageList (330 chroms): 1 millis pass2 - checking and writing primary data (3567 records, 4 fields): 13 millis CompletedMACS2peakCalling