Job ID = 6453969 SRX = SRX1715682 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:36:09 prefetch.2.10.7: 1) Downloading 'SRR3405223'... 2020-06-21T08:36:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:52:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:52:00 prefetch.2.10.7: 1) 'SRR3405223' was downloaded successfully Read 46365619 spots for SRR3405223/SRR3405223.sra Written 46365619 spots for SRR3405223/SRR3405223.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: 00:12:11 46365619 reads; of these: 46365619 (100.00%) were unpaired; of these: 2793750 (6.03%) aligned 0 times 32223285 (69.50%) aligned exactly 1 time 11348584 (24.48%) aligned >1 times 93.97% overall alignment rate Time searching: 00:12:11 Overall time: 00:12:11 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 20 files... [bam_rmdupse_core] 18431214 / 43571869 = 0.4230 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 18:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.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 18:17:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:18: 1000000 INFO @ Sun, 21 Jun 2020 18:17:24: 2000000 INFO @ Sun, 21 Jun 2020 18:17:30: 3000000 INFO @ Sun, 21 Jun 2020 18:17:36: 4000000 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 18:17:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.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 18:17:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:43: 5000000 INFO @ Sun, 21 Jun 2020 18:17:48: 1000000 INFO @ Sun, 21 Jun 2020 18:17:49: 6000000 INFO @ Sun, 21 Jun 2020 18:17:55: 2000000 INFO @ Sun, 21 Jun 2020 18:17:56: 7000000 INFO @ Sun, 21 Jun 2020 18:18:02: 3000000 INFO @ Sun, 21 Jun 2020 18:18:03: 8000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 18:18:09: 4000000 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 18:18:10: 9000000 INFO @ Sun, 21 Jun 2020 18:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.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 18:18:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:16: 5000000 INFO @ Sun, 21 Jun 2020 18:18:17: 10000000 INFO @ Sun, 21 Jun 2020 18:18:19: 1000000 INFO @ Sun, 21 Jun 2020 18:18:24: 6000000 INFO @ Sun, 21 Jun 2020 18:18:24: 11000000 INFO @ Sun, 21 Jun 2020 18:18:26: 2000000 INFO @ Sun, 21 Jun 2020 18:18:31: 7000000 INFO @ Sun, 21 Jun 2020 18:18:31: 12000000 INFO @ Sun, 21 Jun 2020 18:18:34: 3000000 INFO @ Sun, 21 Jun 2020 18:18:38: 8000000 INFO @ Sun, 21 Jun 2020 18:18:39: 13000000 INFO @ Sun, 21 Jun 2020 18:18:41: 4000000 INFO @ Sun, 21 Jun 2020 18:18:45: 9000000 INFO @ Sun, 21 Jun 2020 18:18:46: 14000000 INFO @ Sun, 21 Jun 2020 18:18:48: 5000000 INFO @ Sun, 21 Jun 2020 18:18:52: 10000000 INFO @ Sun, 21 Jun 2020 18:18:53: 15000000 INFO @ Sun, 21 Jun 2020 18:18:55: 6000000 INFO @ Sun, 21 Jun 2020 18:18:59: 11000000 INFO @ Sun, 21 Jun 2020 18:19:00: 16000000 INFO @ Sun, 21 Jun 2020 18:19:02: 7000000 INFO @ Sun, 21 Jun 2020 18:19:06: 12000000 INFO @ Sun, 21 Jun 2020 18:19:08: 17000000 INFO @ Sun, 21 Jun 2020 18:19:10: 8000000 INFO @ Sun, 21 Jun 2020 18:19:13: 13000000 INFO @ Sun, 21 Jun 2020 18:19:15: 18000000 INFO @ Sun, 21 Jun 2020 18:19:17: 9000000 INFO @ Sun, 21 Jun 2020 18:19:20: 14000000 INFO @ Sun, 21 Jun 2020 18:19:22: 19000000 INFO @ Sun, 21 Jun 2020 18:19:23: 10000000 INFO @ Sun, 21 Jun 2020 18:19:27: 15000000 INFO @ Sun, 21 Jun 2020 18:19:30: 20000000 INFO @ Sun, 21 Jun 2020 18:19:31: 11000000 INFO @ Sun, 21 Jun 2020 18:19:34: 16000000 INFO @ Sun, 21 Jun 2020 18:19:38: 12000000 INFO @ Sun, 21 Jun 2020 18:19:38: 21000000 INFO @ Sun, 21 Jun 2020 18:19:42: 17000000 INFO @ Sun, 21 Jun 2020 18:19:45: 13000000 INFO @ Sun, 21 Jun 2020 18:19:46: 22000000 INFO @ Sun, 21 Jun 2020 18:19:48: 18000000 INFO @ Sun, 21 Jun 2020 18:19:52: 14000000 INFO @ Sun, 21 Jun 2020 18:19:52: 23000000 INFO @ Sun, 21 Jun 2020 18:19:55: 19000000 INFO @ Sun, 21 Jun 2020 18:19:58: 15000000 INFO @ Sun, 21 Jun 2020 18:19:59: 24000000 INFO @ Sun, 21 Jun 2020 18:20:02: 20000000 INFO @ Sun, 21 Jun 2020 18:20:05: 16000000 INFO @ Sun, 21 Jun 2020 18:20:05: 25000000 INFO @ Sun, 21 Jun 2020 18:20:07: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:20:07: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:20:07: #1 total tags in treatment: 25140655 INFO @ Sun, 21 Jun 2020 18:20:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:07: #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 18:20:08: #1 tags after filtering in treatment: 25140655 INFO @ Sun, 21 Jun 2020 18:20:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:10: #2 number of paired peaks: 110 WARNING @ Sun, 21 Jun 2020 18:20:10: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:10: 21000000 INFO @ Sun, 21 Jun 2020 18:20:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:10: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:20:10: #2 alternative fragment length(s) may be 1,31,34,58,477,510,535,575 bps INFO @ Sun, 21 Jun 2020 18:20:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.05_model.r WARNING @ Sun, 21 Jun 2020 18:20:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:10: #2 You may need to consider one of the other alternative d(s): 1,31,34,58,477,510,535,575 WARNING @ Sun, 21 Jun 2020 18:20:10: #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 18:20:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:12: 17000000 INFO @ Sun, 21 Jun 2020 18:20:17: 22000000 INFO @ Sun, 21 Jun 2020 18:20:18: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:23: 23000000 INFO @ Sun, 21 Jun 2020 18:20:25: 19000000 INFO @ Sun, 21 Jun 2020 18:20:30: 24000000 INFO @ Sun, 21 Jun 2020 18:20:32: 20000000 INFO @ Sun, 21 Jun 2020 18:20:37: 25000000 INFO @ Sun, 21 Jun 2020 18:20:38: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:20:38: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:20:38: #1 total tags in treatment: 25140655 INFO @ Sun, 21 Jun 2020 18:20:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:38: #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 18:20:39: #1 tags after filtering in treatment: 25140655 INFO @ Sun, 21 Jun 2020 18:20:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:39: 21000000 INFO @ Sun, 21 Jun 2020 18:20:41: #2 number of paired peaks: 110 WARNING @ Sun, 21 Jun 2020 18:20:41: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:41: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:20:41: #2 alternative fragment length(s) may be 1,31,34,58,477,510,535,575 bps INFO @ Sun, 21 Jun 2020 18:20:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.10_model.r WARNING @ Sun, 21 Jun 2020 18:20:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:41: #2 You may need to consider one of the other alternative d(s): 1,31,34,58,477,510,535,575 WARNING @ Sun, 21 Jun 2020 18:20:41: #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 18:20:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:46: 22000000 INFO @ Sun, 21 Jun 2020 18:20:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:52: 23000000 INFO @ Sun, 21 Jun 2020 18:20:58: 24000000 INFO @ Sun, 21 Jun 2020 18:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:04: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:04: 25000000 INFO @ Sun, 21 Jun 2020 18:21:05: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:21:05: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:21:05: #1 total tags in treatment: 25140655 INFO @ Sun, 21 Jun 2020 18:21:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:05: #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 18:21:06: #1 tags after filtering in treatment: 25140655 INFO @ Sun, 21 Jun 2020 18:21:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:08: #2 number of paired peaks: 110 WARNING @ Sun, 21 Jun 2020 18:21:08: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sun, 21 Jun 2020 18:21:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:08: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:21:08: #2 alternative fragment length(s) may be 1,31,34,58,477,510,535,575 bps INFO @ Sun, 21 Jun 2020 18:21:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.20_model.r WARNING @ Sun, 21 Jun 2020 18:21:08: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:08: #2 You may need to consider one of the other alternative d(s): 1,31,34,58,477,510,535,575 WARNING @ Sun, 21 Jun 2020 18:21:08: #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 18:21:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:34: 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。 INFO @ Sun, 21 Jun 2020 18:21:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1715682/SRX1715682.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling