Job ID = 6527771 SRX = SRX2831138 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:19:23 prefetch.2.10.7: 1) Downloading 'SRR5572460'... 2020-06-29T13:19:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:22:43 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:22:43 prefetch.2.10.7: 1) 'SRR5572460' was downloaded successfully Read 29172280 spots for SRR5572460/SRR5572460.sra Written 29172280 spots for SRR5572460/SRR5572460.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: 00:07:43 29172280 reads; of these: 29172280 (100.00%) were unpaired; of these: 3084822 (10.57%) aligned 0 times 20023021 (68.64%) aligned exactly 1 time 6064437 (20.79%) aligned >1 times 89.43% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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 12 files... [bam_rmdupse_core] 3294941 / 26087458 = 0.1263 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 22:44:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.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 22:44:26: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:44:26: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:44:32: 1000000 INFO @ Mon, 29 Jun 2020 22:44:37: 2000000 INFO @ Mon, 29 Jun 2020 22:44:42: 3000000 INFO @ Mon, 29 Jun 2020 22:44:47: 4000000 INFO @ Mon, 29 Jun 2020 22:44:52: 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 22:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.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 22:44:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:44:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:44:57: 6000000 INFO @ Mon, 29 Jun 2020 22:45:03: 7000000 INFO @ Mon, 29 Jun 2020 22:45:03: 1000000 INFO @ Mon, 29 Jun 2020 22:45:09: 8000000 INFO @ Mon, 29 Jun 2020 22:45:10: 2000000 INFO @ Mon, 29 Jun 2020 22:45:15: 9000000 INFO @ Mon, 29 Jun 2020 22:45:16: 3000000 INFO @ Mon, 29 Jun 2020 22:45:21: 10000000 INFO @ Mon, 29 Jun 2020 22:45:23: 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 22:45:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.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 22:45:27: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:45:27: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:45:27: 11000000 INFO @ Mon, 29 Jun 2020 22:45:29: 5000000 INFO @ Mon, 29 Jun 2020 22:45:33: 1000000 INFO @ Mon, 29 Jun 2020 22:45:33: 12000000 INFO @ Mon, 29 Jun 2020 22:45:35: 6000000 INFO @ Mon, 29 Jun 2020 22:45:39: 2000000 INFO @ Mon, 29 Jun 2020 22:45:39: 13000000 INFO @ Mon, 29 Jun 2020 22:45:42: 7000000 INFO @ Mon, 29 Jun 2020 22:45:44: 3000000 INFO @ Mon, 29 Jun 2020 22:45:45: 14000000 INFO @ Mon, 29 Jun 2020 22:45:48: 8000000 INFO @ Mon, 29 Jun 2020 22:45:50: 4000000 INFO @ Mon, 29 Jun 2020 22:45:51: 15000000 INFO @ Mon, 29 Jun 2020 22:45:55: 9000000 INFO @ Mon, 29 Jun 2020 22:45:56: 5000000 INFO @ Mon, 29 Jun 2020 22:45:57: 16000000 INFO @ Mon, 29 Jun 2020 22:46:02: 10000000 INFO @ Mon, 29 Jun 2020 22:46:02: 6000000 INFO @ Mon, 29 Jun 2020 22:46:02: 17000000 INFO @ Mon, 29 Jun 2020 22:46:08: 7000000 INFO @ Mon, 29 Jun 2020 22:46:08: 18000000 INFO @ Mon, 29 Jun 2020 22:46:08: 11000000 INFO @ Mon, 29 Jun 2020 22:46:13: 8000000 INFO @ Mon, 29 Jun 2020 22:46:14: 19000000 INFO @ Mon, 29 Jun 2020 22:46:15: 12000000 INFO @ Mon, 29 Jun 2020 22:46:19: 9000000 INFO @ Mon, 29 Jun 2020 22:46:20: 20000000 INFO @ Mon, 29 Jun 2020 22:46:21: 13000000 INFO @ Mon, 29 Jun 2020 22:46:25: 10000000 INFO @ Mon, 29 Jun 2020 22:46:26: 21000000 INFO @ Mon, 29 Jun 2020 22:46:28: 14000000 INFO @ Mon, 29 Jun 2020 22:46:31: 11000000 INFO @ Mon, 29 Jun 2020 22:46:31: 22000000 INFO @ Mon, 29 Jun 2020 22:46:35: 15000000 INFO @ Mon, 29 Jun 2020 22:46:36: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:46:36: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:46:36: #1 total tags in treatment: 22792517 INFO @ Mon, 29 Jun 2020 22:46:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:46:36: #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 22:46:36: #1 tags after filtering in treatment: 22792517 INFO @ Mon, 29 Jun 2020 22:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:46:36: #1 finished! INFO @ Mon, 29 Jun 2020 22:46:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:46:37: 12000000 INFO @ Mon, 29 Jun 2020 22:46:38: #2 number of paired peaks: 417 WARNING @ Mon, 29 Jun 2020 22:46:38: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Mon, 29 Jun 2020 22:46:38: start model_add_line... INFO @ Mon, 29 Jun 2020 22:46:38: start X-correlation... INFO @ Mon, 29 Jun 2020 22:46:38: end of X-cor INFO @ Mon, 29 Jun 2020 22:46:38: #2 finished! INFO @ Mon, 29 Jun 2020 22:46:38: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:46:38: #2 alternative fragment length(s) may be 2,40,594 bps INFO @ Mon, 29 Jun 2020 22:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.05_model.r WARNING @ Mon, 29 Jun 2020 22:46:38: #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 22:46:38: #2 You may need to consider one of the other alternative d(s): 2,40,594 WARNING @ Mon, 29 Jun 2020 22:46:38: #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 22:46:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:46:41: 16000000 INFO @ Mon, 29 Jun 2020 22:46:43: 13000000 INFO @ Mon, 29 Jun 2020 22:46:48: 17000000 INFO @ Mon, 29 Jun 2020 22:46:49: 14000000 INFO @ Mon, 29 Jun 2020 22:46:54: 18000000 INFO @ Mon, 29 Jun 2020 22:46:55: 15000000 INFO @ Mon, 29 Jun 2020 22:47:00: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:47:01: 16000000 INFO @ Mon, 29 Jun 2020 22:47:07: 20000000 INFO @ Mon, 29 Jun 2020 22:47:07: 17000000 INFO @ Mon, 29 Jun 2020 22:47:13: 18000000 INFO @ Mon, 29 Jun 2020 22:47:14: 21000000 INFO @ Mon, 29 Jun 2020 22:47:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:47:19: 19000000 INFO @ Mon, 29 Jun 2020 22:47:20: 22000000 INFO @ Mon, 29 Jun 2020 22:47:25: 20000000 INFO @ Mon, 29 Jun 2020 22:47:25: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:47:25: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:47:25: #1 total tags in treatment: 22792517 INFO @ Mon, 29 Jun 2020 22:47:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:47:25: #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 22:47:26: #1 tags after filtering in treatment: 22792517 INFO @ Mon, 29 Jun 2020 22:47:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:47:26: #1 finished! INFO @ Mon, 29 Jun 2020 22:47:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:47:27: #2 number of paired peaks: 417 WARNING @ Mon, 29 Jun 2020 22:47:27: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Mon, 29 Jun 2020 22:47:27: start model_add_line... INFO @ Mon, 29 Jun 2020 22:47:27: start X-correlation... INFO @ Mon, 29 Jun 2020 22:47:27: end of X-cor INFO @ Mon, 29 Jun 2020 22:47:27: #2 finished! INFO @ Mon, 29 Jun 2020 22:47:27: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:47:27: #2 alternative fragment length(s) may be 2,40,594 bps INFO @ Mon, 29 Jun 2020 22:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.10_model.r WARNING @ Mon, 29 Jun 2020 22:47:27: #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 22:47:27: #2 You may need to consider one of the other alternative d(s): 2,40,594 WARNING @ Mon, 29 Jun 2020 22:47:27: #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 22:47:27: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:47:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:47:30: 21000000 INFO @ Mon, 29 Jun 2020 22:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.05_summits.bed INFO @ Mon, 29 Jun 2020 22:47:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:47:35: 22000000 INFO @ Mon, 29 Jun 2020 22:47:40: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:47:40: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:47:40: #1 total tags in treatment: 22792517 INFO @ Mon, 29 Jun 2020 22:47:40: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:47:40: #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 22:47:40: #1 tags after filtering in treatment: 22792517 INFO @ Mon, 29 Jun 2020 22:47:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:47:40: #1 finished! INFO @ Mon, 29 Jun 2020 22:47:40: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:47:41: #2 number of paired peaks: 417 WARNING @ Mon, 29 Jun 2020 22:47:41: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Mon, 29 Jun 2020 22:47:41: start model_add_line... INFO @ Mon, 29 Jun 2020 22:47:42: start X-correlation... INFO @ Mon, 29 Jun 2020 22:47:42: end of X-cor INFO @ Mon, 29 Jun 2020 22:47:42: #2 finished! INFO @ Mon, 29 Jun 2020 22:47:42: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:47:42: #2 alternative fragment length(s) may be 2,40,594 bps INFO @ Mon, 29 Jun 2020 22:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.20_model.r WARNING @ Mon, 29 Jun 2020 22:47:42: #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 22:47:42: #2 You may need to consider one of the other alternative d(s): 2,40,594 WARNING @ Mon, 29 Jun 2020 22:47:42: #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 22:47:42: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:47:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:48:03: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:48:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:48:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:48:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:48:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.10_summits.bed INFO @ Mon, 29 Jun 2020 22:48:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:48:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:48:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2831138/SRX2831138.20_summits.bed INFO @ Mon, 29 Jun 2020 22:48:36: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling