Job ID = 6527641 SRX = SRX1837298 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:12:03 prefetch.2.10.7: 1) Downloading 'SRR3657654'... 2020-06-29T13:12:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:58 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:58 prefetch.2.10.7: 1) 'SRR3657654' was downloaded successfully Read 33930162 spots for SRR3657654/SRR3657654.sra Written 33930162 spots for SRR3657654/SRR3657654.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: 00:00:01 Multiseed full-index search: 00:14:29 33930162 reads; of these: 33930162 (100.00%) were unpaired; of these: 4377870 (12.90%) aligned 0 times 10955980 (32.29%) aligned exactly 1 time 18596312 (54.81%) aligned >1 times 87.10% overall alignment rate Time searching: 00:14:30 Overall time: 00:14:30 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 16 files... [bam_rmdupse_core] 6930810 / 29552292 = 0.2345 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 @ Mon, 29 Jun 2020 22:45:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.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 @ Mon, 29 Jun 2020 22:45:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:45:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:45:50: 1000000 INFO @ Mon, 29 Jun 2020 22:45:55: 2000000 INFO @ Mon, 29 Jun 2020 22:46:01: 3000000 INFO @ Mon, 29 Jun 2020 22:46:06: 4000000 INFO @ Mon, 29 Jun 2020 22:46:12: 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 @ Mon, 29 Jun 2020 22:46:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.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 @ Mon, 29 Jun 2020 22:46:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:46:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:46:18: 6000000 INFO @ Mon, 29 Jun 2020 22:46:21: 1000000 INFO @ Mon, 29 Jun 2020 22:46:25: 7000000 INFO @ Mon, 29 Jun 2020 22:46:28: 2000000 INFO @ Mon, 29 Jun 2020 22:46:31: 8000000 INFO @ Mon, 29 Jun 2020 22:46:34: 3000000 INFO @ Mon, 29 Jun 2020 22:46:38: 9000000 INFO @ Mon, 29 Jun 2020 22:46:41: 4000000 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 @ Mon, 29 Jun 2020 22:46:44: 10000000 INFO @ Mon, 29 Jun 2020 22:46:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.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 @ Mon, 29 Jun 2020 22:46:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:46:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:46:47: 5000000 INFO @ Mon, 29 Jun 2020 22:46:51: 11000000 INFO @ Mon, 29 Jun 2020 22:46:51: 1000000 INFO @ Mon, 29 Jun 2020 22:46:54: 6000000 INFO @ Mon, 29 Jun 2020 22:46:57: 2000000 INFO @ Mon, 29 Jun 2020 22:46:57: 12000000 INFO @ Mon, 29 Jun 2020 22:47:00: 7000000 INFO @ Mon, 29 Jun 2020 22:47:03: 3000000 INFO @ Mon, 29 Jun 2020 22:47:03: 13000000 INFO @ Mon, 29 Jun 2020 22:47:07: 8000000 INFO @ Mon, 29 Jun 2020 22:47:10: 4000000 INFO @ Mon, 29 Jun 2020 22:47:10: 14000000 INFO @ Mon, 29 Jun 2020 22:47:14: 9000000 INFO @ Mon, 29 Jun 2020 22:47:16: 5000000 INFO @ Mon, 29 Jun 2020 22:47:16: 15000000 INFO @ Mon, 29 Jun 2020 22:47:20: 10000000 INFO @ Mon, 29 Jun 2020 22:47:22: 6000000 INFO @ Mon, 29 Jun 2020 22:47:22: 16000000 INFO @ Mon, 29 Jun 2020 22:47:27: 11000000 INFO @ Mon, 29 Jun 2020 22:47:28: 7000000 INFO @ Mon, 29 Jun 2020 22:47:29: 17000000 INFO @ Mon, 29 Jun 2020 22:47:33: 12000000 INFO @ Mon, 29 Jun 2020 22:47:34: 8000000 INFO @ Mon, 29 Jun 2020 22:47:35: 18000000 INFO @ Mon, 29 Jun 2020 22:47:40: 13000000 INFO @ Mon, 29 Jun 2020 22:47:40: 9000000 INFO @ Mon, 29 Jun 2020 22:47:42: 19000000 INFO @ Mon, 29 Jun 2020 22:47:46: 14000000 INFO @ Mon, 29 Jun 2020 22:47:47: 10000000 INFO @ Mon, 29 Jun 2020 22:47:48: 20000000 INFO @ Mon, 29 Jun 2020 22:47:53: 11000000 INFO @ Mon, 29 Jun 2020 22:47:53: 15000000 INFO @ Mon, 29 Jun 2020 22:47:54: 21000000 INFO @ Mon, 29 Jun 2020 22:47:59: 12000000 INFO @ Mon, 29 Jun 2020 22:47:59: 16000000 INFO @ Mon, 29 Jun 2020 22:48:01: 22000000 INFO @ Mon, 29 Jun 2020 22:48:05: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:48:05: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:48:05: #1 total tags in treatment: 22621482 INFO @ Mon, 29 Jun 2020 22:48:05: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:48:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:48:05: 13000000 INFO @ Mon, 29 Jun 2020 22:48:05: #1 tags after filtering in treatment: 22621482 INFO @ Mon, 29 Jun 2020 22:48:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:48:05: #1 finished! INFO @ Mon, 29 Jun 2020 22:48:05: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:48:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:48:06: 17000000 INFO @ Mon, 29 Jun 2020 22:48:07: #2 number of paired peaks: 966 WARNING @ Mon, 29 Jun 2020 22:48:07: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Mon, 29 Jun 2020 22:48:07: start model_add_line... INFO @ Mon, 29 Jun 2020 22:48:07: start X-correlation... INFO @ Mon, 29 Jun 2020 22:48:07: end of X-cor INFO @ Mon, 29 Jun 2020 22:48:07: #2 finished! INFO @ Mon, 29 Jun 2020 22:48:07: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:48:07: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 29 Jun 2020 22:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.05_model.r WARNING @ Mon, 29 Jun 2020 22:48:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:48:07: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 29 Jun 2020 22:48:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:48:07: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:48:11: 14000000 INFO @ Mon, 29 Jun 2020 22:48:13: 18000000 INFO @ Mon, 29 Jun 2020 22:48:17: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:48:19: 19000000 INFO @ Mon, 29 Jun 2020 22:48:23: 16000000 INFO @ Mon, 29 Jun 2020 22:48:26: 20000000 INFO @ Mon, 29 Jun 2020 22:48:29: 17000000 INFO @ Mon, 29 Jun 2020 22:48:33: 21000000 INFO @ Mon, 29 Jun 2020 22:48:35: 18000000 INFO @ Mon, 29 Jun 2020 22:48:40: 22000000 INFO @ Mon, 29 Jun 2020 22:48:41: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:48:41: 19000000 INFO @ Mon, 29 Jun 2020 22:48:44: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:48:44: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:48:44: #1 total tags in treatment: 22621482 INFO @ Mon, 29 Jun 2020 22:48:44: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:48:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:48:44: #1 tags after filtering in treatment: 22621482 INFO @ Mon, 29 Jun 2020 22:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:48:44: #1 finished! INFO @ Mon, 29 Jun 2020 22:48:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:48:46: #2 number of paired peaks: 966 WARNING @ Mon, 29 Jun 2020 22:48:46: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Mon, 29 Jun 2020 22:48:46: start model_add_line... INFO @ Mon, 29 Jun 2020 22:48:46: start X-correlation... INFO @ Mon, 29 Jun 2020 22:48:46: end of X-cor INFO @ Mon, 29 Jun 2020 22:48:46: #2 finished! INFO @ Mon, 29 Jun 2020 22:48:46: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:48:46: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 29 Jun 2020 22:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.10_model.r WARNING @ Mon, 29 Jun 2020 22:48:46: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:48:46: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 29 Jun 2020 22:48:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:48:46: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:48:47: 20000000 INFO @ Mon, 29 Jun 2020 22:48:53: 21000000 INFO @ Mon, 29 Jun 2020 22:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.05_summits.bed INFO @ Mon, 29 Jun 2020 22:48:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:48:58: 22000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:49:02: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:49:02: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:49:02: #1 total tags in treatment: 22621482 INFO @ Mon, 29 Jun 2020 22:49:02: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:49:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:49:02: #1 tags after filtering in treatment: 22621482 INFO @ Mon, 29 Jun 2020 22:49:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:49:02: #1 finished! INFO @ Mon, 29 Jun 2020 22:49:02: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:49:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:49:04: #2 number of paired peaks: 966 WARNING @ Mon, 29 Jun 2020 22:49:04: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Mon, 29 Jun 2020 22:49:04: start model_add_line... INFO @ Mon, 29 Jun 2020 22:49:04: start X-correlation... INFO @ Mon, 29 Jun 2020 22:49:04: end of X-cor INFO @ Mon, 29 Jun 2020 22:49:04: #2 finished! INFO @ Mon, 29 Jun 2020 22:49:04: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:49:04: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 29 Jun 2020 22:49:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.20_model.r WARNING @ Mon, 29 Jun 2020 22:49:04: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:49:04: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 29 Jun 2020 22:49:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:49:04: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:49:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:49:20: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.10_summits.bed INFO @ Mon, 29 Jun 2020 22:49:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:49:38: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1837298/SRX1837298.20_summits.bed INFO @ Mon, 29 Jun 2020 22:49:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling