Job ID = 6457654 SRX = SRX467056 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:35:55 prefetch.2.10.7: 1) Downloading 'SRR1164480'... 2020-06-21T11:35:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:41:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:41:10 prefetch.2.10.7: 1) 'SRR1164480' was downloaded successfully Read 40621839 spots for SRR1164480/SRR1164480.sra Written 40621839 spots for SRR1164480/SRR1164480.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: 00:14:49 40621839 reads; of these: 40621839 (100.00%) were unpaired; of these: 2828737 (6.96%) aligned 0 times 22319515 (54.94%) aligned exactly 1 time 15473587 (38.09%) aligned >1 times 93.04% overall alignment rate Time searching: 00:14:49 Overall time: 00:14:49 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 16 files... [bam_rmdupse_core] 16136039 / 37793102 = 0.4270 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 21:07:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.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 21:07:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:10: 1000000 INFO @ Sun, 21 Jun 2020 21:07:15: 2000000 INFO @ Sun, 21 Jun 2020 21:07:20: 3000000 INFO @ Sun, 21 Jun 2020 21:07:25: 4000000 INFO @ Sun, 21 Jun 2020 21:07:30: 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 21:07:34: 6000000 INFO @ Sun, 21 Jun 2020 21:07:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.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 21:07:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:39: 7000000 INFO @ Sun, 21 Jun 2020 21:07:41: 1000000 INFO @ Sun, 21 Jun 2020 21:07:44: 8000000 INFO @ Sun, 21 Jun 2020 21:07:46: 2000000 INFO @ Sun, 21 Jun 2020 21:07:49: 9000000 INFO @ Sun, 21 Jun 2020 21:07:52: 3000000 INFO @ Sun, 21 Jun 2020 21:07:53: 10000000 INFO @ Sun, 21 Jun 2020 21:07:57: 4000000 INFO @ Sun, 21 Jun 2020 21:07:58: 11000000 INFO @ Sun, 21 Jun 2020 21:08:02: 5000000 INFO @ Sun, 21 Jun 2020 21:08:03: 12000000 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 21:08:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.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 21:08:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:08:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:08:07: 6000000 INFO @ Sun, 21 Jun 2020 21:08:08: 13000000 INFO @ Sun, 21 Jun 2020 21:08:11: 1000000 INFO @ Sun, 21 Jun 2020 21:08:12: 7000000 INFO @ Sun, 21 Jun 2020 21:08:13: 14000000 INFO @ Sun, 21 Jun 2020 21:08:16: 2000000 INFO @ Sun, 21 Jun 2020 21:08:17: 8000000 INFO @ Sun, 21 Jun 2020 21:08:17: 15000000 INFO @ Sun, 21 Jun 2020 21:08:22: 3000000 INFO @ Sun, 21 Jun 2020 21:08:22: 16000000 INFO @ Sun, 21 Jun 2020 21:08:23: 9000000 INFO @ Sun, 21 Jun 2020 21:08:27: 4000000 INFO @ Sun, 21 Jun 2020 21:08:28: 17000000 INFO @ Sun, 21 Jun 2020 21:08:28: 10000000 INFO @ Sun, 21 Jun 2020 21:08:32: 5000000 INFO @ Sun, 21 Jun 2020 21:08:33: 18000000 INFO @ Sun, 21 Jun 2020 21:08:33: 11000000 INFO @ Sun, 21 Jun 2020 21:08:38: 6000000 INFO @ Sun, 21 Jun 2020 21:08:38: 19000000 INFO @ Sun, 21 Jun 2020 21:08:38: 12000000 INFO @ Sun, 21 Jun 2020 21:08:43: 20000000 INFO @ Sun, 21 Jun 2020 21:08:43: 7000000 INFO @ Sun, 21 Jun 2020 21:08:44: 13000000 INFO @ Sun, 21 Jun 2020 21:08:48: 21000000 INFO @ Sun, 21 Jun 2020 21:08:48: 8000000 INFO @ Sun, 21 Jun 2020 21:08:49: 14000000 INFO @ Sun, 21 Jun 2020 21:08:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:08:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:08:51: #1 total tags in treatment: 21657063 INFO @ Sun, 21 Jun 2020 21:08:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:08:51: #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 21:08:52: #1 tags after filtering in treatment: 21657063 INFO @ Sun, 21 Jun 2020 21:08:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:08:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:08:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:08:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:08:53: 9000000 INFO @ Sun, 21 Jun 2020 21:08:54: #2 number of paired peaks: 406 WARNING @ Sun, 21 Jun 2020 21:08:54: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Sun, 21 Jun 2020 21:08:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:08:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:08:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:08:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:08:54: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:08:54: #2 alternative fragment length(s) may be 2,571,588 bps INFO @ Sun, 21 Jun 2020 21:08:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.05_model.r WARNING @ Sun, 21 Jun 2020 21:08:54: #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 21:08:54: #2 You may need to consider one of the other alternative d(s): 2,571,588 WARNING @ Sun, 21 Jun 2020 21:08:54: #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 21:08:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:08:54: 15000000 INFO @ Sun, 21 Jun 2020 21:08:59: 10000000 INFO @ Sun, 21 Jun 2020 21:08:59: 16000000 INFO @ Sun, 21 Jun 2020 21:09:04: 11000000 INFO @ Sun, 21 Jun 2020 21:09:05: 17000000 INFO @ Sun, 21 Jun 2020 21:09:09: 12000000 INFO @ Sun, 21 Jun 2020 21:09:11: 18000000 INFO @ Sun, 21 Jun 2020 21:09:14: 13000000 INFO @ Sun, 21 Jun 2020 21:09:16: 19000000 INFO @ Sun, 21 Jun 2020 21:09:20: 14000000 INFO @ Sun, 21 Jun 2020 21:09:21: 20000000 INFO @ Sun, 21 Jun 2020 21:09:25: 15000000 INFO @ Sun, 21 Jun 2020 21:09:27: 21000000 INFO @ Sun, 21 Jun 2020 21:09:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:09:30: 16000000 INFO @ Sun, 21 Jun 2020 21:09:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:09:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:09:30: #1 total tags in treatment: 21657063 INFO @ Sun, 21 Jun 2020 21:09:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:30: #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 21:09:31: #1 tags after filtering in treatment: 21657063 INFO @ Sun, 21 Jun 2020 21:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:33: #2 number of paired peaks: 406 WARNING @ Sun, 21 Jun 2020 21:09:33: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Sun, 21 Jun 2020 21:09:33: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:33: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:33: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:33: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:33: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:09:33: #2 alternative fragment length(s) may be 2,571,588 bps INFO @ Sun, 21 Jun 2020 21:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.10_model.r WARNING @ Sun, 21 Jun 2020 21:09:33: #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 21:09:33: #2 You may need to consider one of the other alternative d(s): 2,571,588 WARNING @ Sun, 21 Jun 2020 21:09:33: #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 21:09:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:09:35: 17000000 INFO @ Sun, 21 Jun 2020 21:09:40: 18000000 INFO @ Sun, 21 Jun 2020 21:09:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:09:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:09:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.05_summits.bed INFO @ Sun, 21 Jun 2020 21:09:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:09:45: 19000000 INFO @ Sun, 21 Jun 2020 21:09:50: 20000000 INFO @ Sun, 21 Jun 2020 21:09:55: 21000000 INFO @ Sun, 21 Jun 2020 21:09:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:09:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:09:59: #1 total tags in treatment: 21657063 INFO @ Sun, 21 Jun 2020 21:09:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:59: #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 21:10:00: #1 tags after filtering in treatment: 21657063 INFO @ Sun, 21 Jun 2020 21:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:10:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:10:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:10:02: #2 number of paired peaks: 406 WARNING @ Sun, 21 Jun 2020 21:10:02: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Sun, 21 Jun 2020 21:10:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:10:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:10:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:10:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:10:02: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:10:02: #2 alternative fragment length(s) may be 2,571,588 bps INFO @ Sun, 21 Jun 2020 21:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.20_model.r WARNING @ Sun, 21 Jun 2020 21:10:02: #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 21:10:02: #2 You may need to consider one of the other alternative d(s): 2,571,588 WARNING @ Sun, 21 Jun 2020 21:10:02: #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 21:10:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:10:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:10:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:10:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.10_summits.bed INFO @ Sun, 21 Jun 2020 21:10:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:10:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467056/SRX467056.20_summits.bed INFO @ Sun, 21 Jun 2020 21:10:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。