Job ID = 6453626 SRX = SRX1300695 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:20:47 prefetch.2.10.7: 1) Downloading 'SRR2548371'... 2020-06-21T08:20:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:25:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:25:26 prefetch.2.10.7: 1) 'SRR2548371' was downloaded successfully Read 26825146 spots for SRR2548371/SRR2548371.sra Written 26825146 spots for SRR2548371/SRR2548371.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: 00:07:20 26825146 reads; of these: 26825146 (100.00%) were unpaired; of these: 1808814 (6.74%) aligned 0 times 18090767 (67.44%) aligned exactly 1 time 6925565 (25.82%) aligned >1 times 93.26% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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 12 files... [bam_rmdupse_core] 4254146 / 25016332 = 0.1701 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 17:42:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.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 17:42:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:42:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:42:32: 1000000 INFO @ Sun, 21 Jun 2020 17:42:39: 2000000 INFO @ Sun, 21 Jun 2020 17:42:47: 3000000 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 17:42:54: 4000000 INFO @ Sun, 21 Jun 2020 17:42:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.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 17:42:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:42:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:02: 5000000 INFO @ Sun, 21 Jun 2020 17:43:02: 1000000 INFO @ Sun, 21 Jun 2020 17:43:09: 2000000 INFO @ Sun, 21 Jun 2020 17:43:09: 6000000 INFO @ Sun, 21 Jun 2020 17:43:17: 3000000 INFO @ Sun, 21 Jun 2020 17:43:17: 7000000 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 17:43:24: 4000000 INFO @ Sun, 21 Jun 2020 17:43:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.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 17:43:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:43:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:24: 8000000 INFO @ Sun, 21 Jun 2020 17:43:32: 1000000 INFO @ Sun, 21 Jun 2020 17:43:32: 5000000 INFO @ Sun, 21 Jun 2020 17:43:32: 9000000 INFO @ Sun, 21 Jun 2020 17:43:39: 2000000 INFO @ Sun, 21 Jun 2020 17:43:39: 6000000 INFO @ Sun, 21 Jun 2020 17:43:40: 10000000 INFO @ Sun, 21 Jun 2020 17:43:47: 3000000 INFO @ Sun, 21 Jun 2020 17:43:47: 7000000 INFO @ Sun, 21 Jun 2020 17:43:47: 11000000 INFO @ Sun, 21 Jun 2020 17:43:54: 4000000 INFO @ Sun, 21 Jun 2020 17:43:55: 8000000 INFO @ Sun, 21 Jun 2020 17:43:55: 12000000 INFO @ Sun, 21 Jun 2020 17:44:01: 5000000 INFO @ Sun, 21 Jun 2020 17:44:02: 13000000 INFO @ Sun, 21 Jun 2020 17:44:02: 9000000 INFO @ Sun, 21 Jun 2020 17:44:08: 6000000 INFO @ Sun, 21 Jun 2020 17:44:10: 14000000 INFO @ Sun, 21 Jun 2020 17:44:10: 10000000 INFO @ Sun, 21 Jun 2020 17:44:15: 7000000 INFO @ Sun, 21 Jun 2020 17:44:18: 15000000 INFO @ Sun, 21 Jun 2020 17:44:18: 11000000 INFO @ Sun, 21 Jun 2020 17:44:23: 8000000 INFO @ Sun, 21 Jun 2020 17:44:25: 12000000 INFO @ Sun, 21 Jun 2020 17:44:25: 16000000 INFO @ Sun, 21 Jun 2020 17:44:30: 9000000 INFO @ Sun, 21 Jun 2020 17:44:32: 13000000 INFO @ Sun, 21 Jun 2020 17:44:33: 17000000 INFO @ Sun, 21 Jun 2020 17:44:37: 10000000 INFO @ Sun, 21 Jun 2020 17:44:39: 14000000 INFO @ Sun, 21 Jun 2020 17:44:40: 18000000 INFO @ Sun, 21 Jun 2020 17:44:44: 11000000 INFO @ Sun, 21 Jun 2020 17:44:46: 15000000 INFO @ Sun, 21 Jun 2020 17:44:47: 19000000 INFO @ Sun, 21 Jun 2020 17:44:51: 12000000 INFO @ Sun, 21 Jun 2020 17:44:53: 16000000 INFO @ Sun, 21 Jun 2020 17:44:54: 20000000 INFO @ Sun, 21 Jun 2020 17:44:58: 13000000 INFO @ Sun, 21 Jun 2020 17:45:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:45:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:45:00: #1 total tags in treatment: 20762186 INFO @ Sun, 21 Jun 2020 17:45:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:00: #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 17:45:00: 17000000 INFO @ Sun, 21 Jun 2020 17:45:01: #1 tags after filtering in treatment: 20762186 INFO @ Sun, 21 Jun 2020 17:45:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:03: #2 number of paired peaks: 467 WARNING @ Sun, 21 Jun 2020 17:45:03: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 21 Jun 2020 17:45:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:45:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:03: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:45:03: #2 alternative fragment length(s) may be 2,39,574 bps INFO @ Sun, 21 Jun 2020 17:45:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.05_model.r WARNING @ Sun, 21 Jun 2020 17:45:03: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:45:03: #2 You may need to consider one of the other alternative d(s): 2,39,574 WARNING @ Sun, 21 Jun 2020 17:45:03: #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 17:45:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:45:04: 14000000 INFO @ Sun, 21 Jun 2020 17:45:06: 18000000 INFO @ Sun, 21 Jun 2020 17:45:11: 15000000 INFO @ Sun, 21 Jun 2020 17:45:12: 19000000 INFO @ Sun, 21 Jun 2020 17:45:18: 16000000 INFO @ Sun, 21 Jun 2020 17:45:18: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:45:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:45:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:45:24: #1 total tags in treatment: 20762186 INFO @ Sun, 21 Jun 2020 17:45:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:24: #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 17:45:24: 17000000 INFO @ Sun, 21 Jun 2020 17:45:24: #1 tags after filtering in treatment: 20762186 INFO @ Sun, 21 Jun 2020 17:45:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:26: #2 number of paired peaks: 467 WARNING @ Sun, 21 Jun 2020 17:45:26: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 21 Jun 2020 17:45:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:45:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:26: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:45:26: #2 alternative fragment length(s) may be 2,39,574 bps INFO @ Sun, 21 Jun 2020 17:45:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.10_model.r WARNING @ Sun, 21 Jun 2020 17:45:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:45:26: #2 You may need to consider one of the other alternative d(s): 2,39,574 WARNING @ Sun, 21 Jun 2020 17:45:26: #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 17:45:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:45:30: 18000000 INFO @ Sun, 21 Jun 2020 17:45:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:35: 19000000 INFO @ Sun, 21 Jun 2020 17:45:41: 20000000 INFO @ Sun, 21 Jun 2020 17:45:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:45:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:45:46: #1 total tags in treatment: 20762186 INFO @ Sun, 21 Jun 2020 17:45:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:46: #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 17:45:47: #1 tags after filtering in treatment: 20762186 INFO @ Sun, 21 Jun 2020 17:45:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:47: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:48: #2 number of paired peaks: 467 WARNING @ Sun, 21 Jun 2020 17:45:48: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 21 Jun 2020 17:45:48: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:45:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:49: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:45:49: #2 alternative fragment length(s) may be 2,39,574 bps INFO @ Sun, 21 Jun 2020 17:45:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.20_model.r WARNING @ Sun, 21 Jun 2020 17:45:49: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:45:49: #2 You may need to consider one of the other alternative d(s): 2,39,574 WARNING @ Sun, 21 Jun 2020 17:45:49: #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 17:45:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:45:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.05_summits.bed INFO @ Sun, 21 Jun 2020 17:45:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:45:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:46:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:46:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:46:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.10_summits.bed INFO @ Sun, 21 Jun 2020 17:46:14: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:46:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:46:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:46:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:46:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300695/SRX1300695.20_summits.bed INFO @ Sun, 21 Jun 2020 17:46:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling