Job ID = 6498760 SRX = SRX750083 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:58:34 prefetch.2.10.7: 1) Downloading 'SRR1638778'... 2020-06-25T23:58:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:02:43 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:02:43 prefetch.2.10.7: 1) 'SRR1638778' was downloaded successfully Read 41675031 spots for SRR1638778/SRR1638778.sra Written 41675031 spots for SRR1638778/SRR1638778.sra 2020-06-26T00:05:29 prefetch.2.10.7: 1) Downloading 'SRR1638779'... 2020-06-26T00:05:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:09:11 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:09:11 prefetch.2.10.7: 1) 'SRR1638779' was downloaded successfully Read 34048270 spots for SRR1638779/SRR1638779.sra Written 34048270 spots for SRR1638779/SRR1638779.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: 00:37:31 75723301 reads; of these: 75723301 (100.00%) were unpaired; of these: 4155490 (5.49%) aligned 0 times 48125439 (63.55%) aligned exactly 1 time 23442372 (30.96%) aligned >1 times 94.51% overall alignment rate Time searching: 00:37:31 Overall time: 00:37:31 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 32 files... [bam_rmdupse_core] 54515478 / 71567811 = 0.7617 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 10:06:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.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 10:06:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:06:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:06:08: 1000000 INFO @ Fri, 26 Jun 2020 10:06:13: 2000000 INFO @ Fri, 26 Jun 2020 10:06:18: 3000000 INFO @ Fri, 26 Jun 2020 10:06:23: 4000000 INFO @ Fri, 26 Jun 2020 10:06:28: 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 @ Fri, 26 Jun 2020 10:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.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 10:06:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:06:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:06:33: 6000000 INFO @ Fri, 26 Jun 2020 10:06:38: 1000000 INFO @ Fri, 26 Jun 2020 10:06:39: 7000000 INFO @ Fri, 26 Jun 2020 10:06:44: 8000000 INFO @ Fri, 26 Jun 2020 10:06:44: 2000000 INFO @ Fri, 26 Jun 2020 10:06:49: 9000000 INFO @ Fri, 26 Jun 2020 10:06:50: 3000000 INFO @ Fri, 26 Jun 2020 10:06:54: 10000000 INFO @ Fri, 26 Jun 2020 10:06:56: 4000000 INFO @ Fri, 26 Jun 2020 10:06:59: 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 @ Fri, 26 Jun 2020 10:07:01: 5000000 INFO @ Fri, 26 Jun 2020 10:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.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 10:07:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:07:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:07:05: 12000000 INFO @ Fri, 26 Jun 2020 10:07:07: 6000000 INFO @ Fri, 26 Jun 2020 10:07:08: 1000000 INFO @ Fri, 26 Jun 2020 10:07:10: 13000000 INFO @ Fri, 26 Jun 2020 10:07:13: 7000000 INFO @ Fri, 26 Jun 2020 10:07:14: 2000000 INFO @ Fri, 26 Jun 2020 10:07:16: 14000000 INFO @ Fri, 26 Jun 2020 10:07:19: 8000000 INFO @ Fri, 26 Jun 2020 10:07:20: 3000000 INFO @ Fri, 26 Jun 2020 10:07:22: 15000000 INFO @ Fri, 26 Jun 2020 10:07:24: 9000000 INFO @ Fri, 26 Jun 2020 10:07:27: 4000000 INFO @ Fri, 26 Jun 2020 10:07:28: 16000000 INFO @ Fri, 26 Jun 2020 10:07:30: 10000000 INFO @ Fri, 26 Jun 2020 10:07:33: 5000000 INFO @ Fri, 26 Jun 2020 10:07:34: 17000000 INFO @ Fri, 26 Jun 2020 10:07:34: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 10:07:34: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 10:07:34: #1 total tags in treatment: 17052333 INFO @ Fri, 26 Jun 2020 10:07:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:07:34: #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 10:07:34: #1 tags after filtering in treatment: 17052333 INFO @ Fri, 26 Jun 2020 10:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:07:34: #1 finished! INFO @ Fri, 26 Jun 2020 10:07:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:07:36: 11000000 INFO @ Fri, 26 Jun 2020 10:07:36: #2 number of paired peaks: 1120 INFO @ Fri, 26 Jun 2020 10:07:36: start model_add_line... INFO @ Fri, 26 Jun 2020 10:07:36: start X-correlation... INFO @ Fri, 26 Jun 2020 10:07:36: end of X-cor INFO @ Fri, 26 Jun 2020 10:07:36: #2 finished! INFO @ Fri, 26 Jun 2020 10:07:36: #2 predicted fragment length is 61 bps INFO @ Fri, 26 Jun 2020 10:07:36: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 26 Jun 2020 10:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.05_model.r WARNING @ Fri, 26 Jun 2020 10:07:36: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:07:36: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 26 Jun 2020 10:07:36: #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 10:07:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:07:38: 6000000 INFO @ Fri, 26 Jun 2020 10:07:41: 12000000 INFO @ Fri, 26 Jun 2020 10:07:44: 7000000 INFO @ Fri, 26 Jun 2020 10:07:47: 13000000 INFO @ Fri, 26 Jun 2020 10:07:49: 8000000 INFO @ Fri, 26 Jun 2020 10:07:52: 14000000 INFO @ Fri, 26 Jun 2020 10:07:55: 9000000 INFO @ Fri, 26 Jun 2020 10:07:58: 15000000 INFO @ Fri, 26 Jun 2020 10:08:00: 10000000 INFO @ Fri, 26 Jun 2020 10:08:04: 16000000 INFO @ Fri, 26 Jun 2020 10:08:06: 11000000 INFO @ Fri, 26 Jun 2020 10:08:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:08:09: 17000000 INFO @ Fri, 26 Jun 2020 10:08:10: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 10:08:10: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 10:08:10: #1 total tags in treatment: 17052333 INFO @ Fri, 26 Jun 2020 10:08:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:08:10: #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 10:08:10: #1 tags after filtering in treatment: 17052333 INFO @ Fri, 26 Jun 2020 10:08:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:08:10: #1 finished! INFO @ Fri, 26 Jun 2020 10:08:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:08:11: 12000000 INFO @ Fri, 26 Jun 2020 10:08:11: #2 number of paired peaks: 1120 INFO @ Fri, 26 Jun 2020 10:08:11: start model_add_line... INFO @ Fri, 26 Jun 2020 10:08:12: start X-correlation... INFO @ Fri, 26 Jun 2020 10:08:12: end of X-cor INFO @ Fri, 26 Jun 2020 10:08:12: #2 finished! INFO @ Fri, 26 Jun 2020 10:08:12: #2 predicted fragment length is 61 bps INFO @ Fri, 26 Jun 2020 10:08:12: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 26 Jun 2020 10:08:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.10_model.r WARNING @ Fri, 26 Jun 2020 10:08:12: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:08:12: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 26 Jun 2020 10:08:12: #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 10:08:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:08:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:08:16: 13000000 INFO @ Fri, 26 Jun 2020 10:08:22: 14000000 INFO @ Fri, 26 Jun 2020 10:08:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:08:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:08:27: 15000000 INFO @ Fri, 26 Jun 2020 10:08:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.05_summits.bed INFO @ Fri, 26 Jun 2020 10:08:27: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14212 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:08:32: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:08:38: 17000000 INFO @ Fri, 26 Jun 2020 10:08:38: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 10:08:38: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 10:08:38: #1 total tags in treatment: 17052333 INFO @ Fri, 26 Jun 2020 10:08:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:08:38: #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 10:08:39: #1 tags after filtering in treatment: 17052333 INFO @ Fri, 26 Jun 2020 10:08:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:08:39: #1 finished! INFO @ Fri, 26 Jun 2020 10:08:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:08:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:08:40: #2 number of paired peaks: 1120 INFO @ Fri, 26 Jun 2020 10:08:40: start model_add_line... INFO @ Fri, 26 Jun 2020 10:08:40: start X-correlation... INFO @ Fri, 26 Jun 2020 10:08:40: end of X-cor INFO @ Fri, 26 Jun 2020 10:08:40: #2 finished! INFO @ Fri, 26 Jun 2020 10:08:40: #2 predicted fragment length is 61 bps INFO @ Fri, 26 Jun 2020 10:08:40: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 26 Jun 2020 10:08:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.20_model.r WARNING @ Fri, 26 Jun 2020 10:08:40: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:08:40: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 26 Jun 2020 10:08:40: #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 10:08:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:08:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:08:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:09:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:09:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:09:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.10_summits.bed INFO @ Fri, 26 Jun 2020 10:09:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5607 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:09:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:09:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:09:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:09:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750083/SRX750083.20_summits.bed INFO @ Fri, 26 Jun 2020 10:09:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1896 records, 4 fields): 17 millis CompletedMACS2peakCalling