Job ID = 6527720 SRX = SRX2520634 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:07:35 prefetch.2.10.7: 1) Downloading 'SRR5206753'... 2020-06-29T13:07:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:12:01 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:12:01 prefetch.2.10.7: 1) 'SRR5206753' was downloaded successfully Read 45518238 spots for SRR5206753/SRR5206753.sra Written 45518238 spots for SRR5206753/SRR5206753.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: 00:12:39 45518238 reads; of these: 45518238 (100.00%) were unpaired; of these: 1217545 (2.67%) aligned 0 times 35628288 (78.27%) aligned exactly 1 time 8672405 (19.05%) aligned >1 times 97.33% overall alignment rate Time searching: 00:12:39 Overall time: 00:12:39 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 20 files... [bam_rmdupse_core] 13580781 / 44300693 = 0.3066 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 22:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.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 22:44:37: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:44:37: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:44:43: 1000000 INFO @ Mon, 29 Jun 2020 22:44:49: 2000000 INFO @ Mon, 29 Jun 2020 22:44:54: 3000000 INFO @ Mon, 29 Jun 2020 22:44:59: 4000000 INFO @ Mon, 29 Jun 2020 22:45:05: 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 22:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.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 22:45:07: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:45:07: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:45:10: 6000000 INFO @ Mon, 29 Jun 2020 22:45:12: 1000000 INFO @ Mon, 29 Jun 2020 22:45:15: 7000000 INFO @ Mon, 29 Jun 2020 22:45:17: 2000000 INFO @ Mon, 29 Jun 2020 22:45:21: 8000000 INFO @ Mon, 29 Jun 2020 22:45:22: 3000000 INFO @ Mon, 29 Jun 2020 22:45:26: 9000000 INFO @ Mon, 29 Jun 2020 22:45:27: 4000000 INFO @ Mon, 29 Jun 2020 22:45:31: 5000000 INFO @ Mon, 29 Jun 2020 22:45:31: 10000000 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 22:45:36: 6000000 INFO @ Mon, 29 Jun 2020 22:45:37: 11000000 INFO @ Mon, 29 Jun 2020 22:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.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 22:45:37: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:45:37: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:45:41: 7000000 INFO @ Mon, 29 Jun 2020 22:45:42: 12000000 INFO @ Mon, 29 Jun 2020 22:45:42: 1000000 INFO @ Mon, 29 Jun 2020 22:45:45: 8000000 INFO @ Mon, 29 Jun 2020 22:45:47: 2000000 INFO @ Mon, 29 Jun 2020 22:45:47: 13000000 INFO @ Mon, 29 Jun 2020 22:45:50: 9000000 INFO @ Mon, 29 Jun 2020 22:45:52: 3000000 INFO @ Mon, 29 Jun 2020 22:45:53: 14000000 INFO @ Mon, 29 Jun 2020 22:45:55: 10000000 INFO @ Mon, 29 Jun 2020 22:45:57: 4000000 INFO @ Mon, 29 Jun 2020 22:45:58: 15000000 INFO @ Mon, 29 Jun 2020 22:46:00: 11000000 INFO @ Mon, 29 Jun 2020 22:46:01: 5000000 INFO @ Mon, 29 Jun 2020 22:46:03: 16000000 INFO @ Mon, 29 Jun 2020 22:46:04: 12000000 INFO @ Mon, 29 Jun 2020 22:46:06: 6000000 INFO @ Mon, 29 Jun 2020 22:46:09: 17000000 INFO @ Mon, 29 Jun 2020 22:46:09: 13000000 INFO @ Mon, 29 Jun 2020 22:46:11: 7000000 INFO @ Mon, 29 Jun 2020 22:46:14: 14000000 INFO @ Mon, 29 Jun 2020 22:46:14: 18000000 INFO @ Mon, 29 Jun 2020 22:46:16: 8000000 INFO @ Mon, 29 Jun 2020 22:46:19: 15000000 INFO @ Mon, 29 Jun 2020 22:46:20: 19000000 INFO @ Mon, 29 Jun 2020 22:46:20: 9000000 INFO @ Mon, 29 Jun 2020 22:46:23: 16000000 INFO @ Mon, 29 Jun 2020 22:46:25: 20000000 INFO @ Mon, 29 Jun 2020 22:46:25: 10000000 INFO @ Mon, 29 Jun 2020 22:46:28: 17000000 INFO @ Mon, 29 Jun 2020 22:46:30: 11000000 INFO @ Mon, 29 Jun 2020 22:46:30: 21000000 INFO @ Mon, 29 Jun 2020 22:46:33: 18000000 INFO @ Mon, 29 Jun 2020 22:46:35: 12000000 INFO @ Mon, 29 Jun 2020 22:46:36: 22000000 INFO @ Mon, 29 Jun 2020 22:46:38: 19000000 INFO @ Mon, 29 Jun 2020 22:46:40: 13000000 INFO @ Mon, 29 Jun 2020 22:46:41: 23000000 INFO @ Mon, 29 Jun 2020 22:46:43: 20000000 INFO @ Mon, 29 Jun 2020 22:46:44: 14000000 INFO @ Mon, 29 Jun 2020 22:46:46: 24000000 INFO @ Mon, 29 Jun 2020 22:46:47: 21000000 INFO @ Mon, 29 Jun 2020 22:46:49: 15000000 INFO @ Mon, 29 Jun 2020 22:46:52: 25000000 INFO @ Mon, 29 Jun 2020 22:46:52: 22000000 INFO @ Mon, 29 Jun 2020 22:46:54: 16000000 INFO @ Mon, 29 Jun 2020 22:46:57: 23000000 INFO @ Mon, 29 Jun 2020 22:46:57: 26000000 INFO @ Mon, 29 Jun 2020 22:46:59: 17000000 INFO @ Mon, 29 Jun 2020 22:47:02: 24000000 INFO @ Mon, 29 Jun 2020 22:47:03: 27000000 INFO @ Mon, 29 Jun 2020 22:47:04: 18000000 INFO @ Mon, 29 Jun 2020 22:47:06: 25000000 INFO @ Mon, 29 Jun 2020 22:47:08: 28000000 INFO @ Mon, 29 Jun 2020 22:47:09: 19000000 INFO @ Mon, 29 Jun 2020 22:47:11: 26000000 INFO @ Mon, 29 Jun 2020 22:47:13: 20000000 INFO @ Mon, 29 Jun 2020 22:47:14: 29000000 INFO @ Mon, 29 Jun 2020 22:47:16: 27000000 INFO @ Mon, 29 Jun 2020 22:47:18: 21000000 INFO @ Mon, 29 Jun 2020 22:47:19: 30000000 INFO @ Mon, 29 Jun 2020 22:47:21: 28000000 INFO @ Mon, 29 Jun 2020 22:47:23: 22000000 INFO @ Mon, 29 Jun 2020 22:47:23: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:47:23: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:47:23: #1 total tags in treatment: 30719912 INFO @ Mon, 29 Jun 2020 22:47:23: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:47:23: #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 22:47:24: #1 tags after filtering in treatment: 30719912 INFO @ Mon, 29 Jun 2020 22:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:47:24: #1 finished! INFO @ Mon, 29 Jun 2020 22:47:24: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:47:26: #2 number of paired peaks: 315 WARNING @ Mon, 29 Jun 2020 22:47:26: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Mon, 29 Jun 2020 22:47:26: start model_add_line... INFO @ Mon, 29 Jun 2020 22:47:26: start X-correlation... INFO @ Mon, 29 Jun 2020 22:47:26: end of X-cor INFO @ Mon, 29 Jun 2020 22:47:26: #2 finished! INFO @ Mon, 29 Jun 2020 22:47:26: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 22:47:26: #2 alternative fragment length(s) may be 1,11,43,575 bps INFO @ Mon, 29 Jun 2020 22:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.05_model.r WARNING @ Mon, 29 Jun 2020 22:47:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:47:26: #2 You may need to consider one of the other alternative d(s): 1,11,43,575 WARNING @ Mon, 29 Jun 2020 22:47:26: #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 22:47:26: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:47:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:47:26: 29000000 INFO @ Mon, 29 Jun 2020 22:47:28: 23000000 INFO @ Mon, 29 Jun 2020 22:47:31: 30000000 INFO @ Mon, 29 Jun 2020 22:47:32: 24000000 INFO @ Mon, 29 Jun 2020 22:47:34: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:47:34: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:47:34: #1 total tags in treatment: 30719912 INFO @ Mon, 29 Jun 2020 22:47:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:47:34: #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 22:47:35: #1 tags after filtering in treatment: 30719912 INFO @ Mon, 29 Jun 2020 22:47:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:47:35: #1 finished! INFO @ Mon, 29 Jun 2020 22:47:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:47:37: #2 number of paired peaks: 315 WARNING @ Mon, 29 Jun 2020 22:47:37: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Mon, 29 Jun 2020 22:47:37: start model_add_line... INFO @ Mon, 29 Jun 2020 22:47:37: start X-correlation... INFO @ Mon, 29 Jun 2020 22:47:37: end of X-cor INFO @ Mon, 29 Jun 2020 22:47:37: #2 finished! INFO @ Mon, 29 Jun 2020 22:47:37: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 22:47:37: #2 alternative fragment length(s) may be 1,11,43,575 bps INFO @ Mon, 29 Jun 2020 22:47:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.10_model.r WARNING @ Mon, 29 Jun 2020 22:47:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:47:37: #2 You may need to consider one of the other alternative d(s): 1,11,43,575 WARNING @ Mon, 29 Jun 2020 22:47:37: #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 22:47:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:47:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:47:37: 25000000 INFO @ Mon, 29 Jun 2020 22:47:42: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:47:47: 27000000 INFO @ Mon, 29 Jun 2020 22:47:51: 28000000 INFO @ Mon, 29 Jun 2020 22:47:56: 29000000 INFO @ Mon, 29 Jun 2020 22:48:01: 30000000 INFO @ Mon, 29 Jun 2020 22:48:04: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:48:04: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:48:04: #1 total tags in treatment: 30719912 INFO @ Mon, 29 Jun 2020 22:48:04: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:48:04: #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: #1 tags after filtering in treatment: 30719912 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 22:48:07: #2 number of paired peaks: 315 WARNING @ Mon, 29 Jun 2020 22:48:07: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 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 1 bps INFO @ Mon, 29 Jun 2020 22:48:07: #2 alternative fragment length(s) may be 1,11,43,575 bps INFO @ Mon, 29 Jun 2020 22:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.20_model.r WARNING @ Mon, 29 Jun 2020 22:48:07: #2 Since the d (1) 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): 1,11,43,575 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 22:48:12: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:48:23: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.05_summits.bed INFO @ Mon, 29 Jun 2020 22:48:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:48:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:48:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:48:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.10_summits.bed INFO @ Mon, 29 Jun 2020 22:48:44: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:48:53: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:49:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:49:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:49:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2520634/SRX2520634.20_summits.bed INFO @ Mon, 29 Jun 2020 22:49:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling