Job ID = 6453763 SRX = SRX146994 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:45:17 prefetch.2.10.7: 1) Downloading 'SRR495368'... 2020-06-21T08:45:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:56:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:56:17 prefetch.2.10.7: 1) 'SRR495368' was downloaded successfully Read 59200042 spots for SRR495368/SRR495368.sra Written 59200042 spots for SRR495368/SRR495368.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: 00:09:44 59200042 reads; of these: 59200042 (100.00%) were unpaired; of these: 16909465 (28.56%) aligned 0 times 32585348 (55.04%) aligned exactly 1 time 9705229 (16.39%) aligned >1 times 71.44% overall alignment rate Time searching: 00:09:44 Overall time: 00:09:44 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 12 files... [bam_rmdupse_core] 11624449 / 42290577 = 0.2749 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 18:16:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.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 18:16:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:45: 1000000 INFO @ Sun, 21 Jun 2020 18:16:50: 2000000 INFO @ Sun, 21 Jun 2020 18:16:55: 3000000 INFO @ Sun, 21 Jun 2020 18:17:00: 4000000 INFO @ Sun, 21 Jun 2020 18:17:06: 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 18:17:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.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 18:17:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:11: 6000000 INFO @ Sun, 21 Jun 2020 18:17:15: 1000000 INFO @ Sun, 21 Jun 2020 18:17:16: 7000000 INFO @ Sun, 21 Jun 2020 18:17:20: 2000000 INFO @ Sun, 21 Jun 2020 18:17:21: 8000000 INFO @ Sun, 21 Jun 2020 18:17:25: 3000000 INFO @ Sun, 21 Jun 2020 18:17:26: 9000000 INFO @ Sun, 21 Jun 2020 18:17:31: 4000000 INFO @ Sun, 21 Jun 2020 18:17:32: 10000000 INFO @ Sun, 21 Jun 2020 18:17:36: 5000000 INFO @ Sun, 21 Jun 2020 18:17:37: 11000000 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 18:17:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.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 18:17:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:41: 6000000 INFO @ Sun, 21 Jun 2020 18:17:42: 12000000 INFO @ Sun, 21 Jun 2020 18:17:45: 1000000 INFO @ Sun, 21 Jun 2020 18:17:47: 7000000 INFO @ Sun, 21 Jun 2020 18:17:47: 13000000 INFO @ Sun, 21 Jun 2020 18:17:51: 2000000 INFO @ Sun, 21 Jun 2020 18:17:52: 8000000 INFO @ Sun, 21 Jun 2020 18:17:53: 14000000 INFO @ Sun, 21 Jun 2020 18:17:57: 3000000 INFO @ Sun, 21 Jun 2020 18:17:57: 9000000 INFO @ Sun, 21 Jun 2020 18:17:58: 15000000 INFO @ Sun, 21 Jun 2020 18:18:02: 4000000 INFO @ Sun, 21 Jun 2020 18:18:03: 10000000 INFO @ Sun, 21 Jun 2020 18:18:03: 16000000 INFO @ Sun, 21 Jun 2020 18:18:07: 5000000 INFO @ Sun, 21 Jun 2020 18:18:08: 11000000 INFO @ Sun, 21 Jun 2020 18:18:08: 17000000 INFO @ Sun, 21 Jun 2020 18:18:13: 6000000 INFO @ Sun, 21 Jun 2020 18:18:14: 12000000 INFO @ Sun, 21 Jun 2020 18:18:14: 18000000 INFO @ Sun, 21 Jun 2020 18:18:18: 7000000 INFO @ Sun, 21 Jun 2020 18:18:19: 13000000 INFO @ Sun, 21 Jun 2020 18:18:19: 19000000 INFO @ Sun, 21 Jun 2020 18:18:23: 8000000 INFO @ Sun, 21 Jun 2020 18:18:24: 14000000 INFO @ Sun, 21 Jun 2020 18:18:24: 20000000 INFO @ Sun, 21 Jun 2020 18:18:28: 9000000 INFO @ Sun, 21 Jun 2020 18:18:29: 15000000 INFO @ Sun, 21 Jun 2020 18:18:29: 21000000 INFO @ Sun, 21 Jun 2020 18:18:34: 10000000 INFO @ Sun, 21 Jun 2020 18:18:34: 16000000 INFO @ Sun, 21 Jun 2020 18:18:35: 22000000 INFO @ Sun, 21 Jun 2020 18:18:39: 11000000 INFO @ Sun, 21 Jun 2020 18:18:39: 17000000 INFO @ Sun, 21 Jun 2020 18:18:40: 23000000 INFO @ Sun, 21 Jun 2020 18:18:44: 12000000 INFO @ Sun, 21 Jun 2020 18:18:44: 18000000 INFO @ Sun, 21 Jun 2020 18:18:45: 24000000 INFO @ Sun, 21 Jun 2020 18:18:49: 13000000 INFO @ Sun, 21 Jun 2020 18:18:49: 19000000 INFO @ Sun, 21 Jun 2020 18:18:50: 25000000 INFO @ Sun, 21 Jun 2020 18:18:54: 14000000 INFO @ Sun, 21 Jun 2020 18:18:55: 20000000 INFO @ Sun, 21 Jun 2020 18:18:56: 26000000 INFO @ Sun, 21 Jun 2020 18:18:59: 15000000 INFO @ Sun, 21 Jun 2020 18:19:00: 21000000 INFO @ Sun, 21 Jun 2020 18:19:01: 27000000 INFO @ Sun, 21 Jun 2020 18:19:04: 16000000 INFO @ Sun, 21 Jun 2020 18:19:05: 22000000 INFO @ Sun, 21 Jun 2020 18:19:06: 28000000 INFO @ Sun, 21 Jun 2020 18:19:09: 17000000 INFO @ Sun, 21 Jun 2020 18:19:10: 23000000 INFO @ Sun, 21 Jun 2020 18:19:12: 29000000 INFO @ Sun, 21 Jun 2020 18:19:14: 18000000 INFO @ Sun, 21 Jun 2020 18:19:16: 24000000 INFO @ Sun, 21 Jun 2020 18:19:17: 30000000 INFO @ Sun, 21 Jun 2020 18:19:20: 19000000 INFO @ Sun, 21 Jun 2020 18:19:21: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:19:21: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:19:21: #1 total tags in treatment: 30666128 INFO @ Sun, 21 Jun 2020 18:19:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:21: #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 18:19:21: 25000000 INFO @ Sun, 21 Jun 2020 18:19:22: #1 tags after filtering in treatment: 30666107 INFO @ Sun, 21 Jun 2020 18:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:23: #2 number of paired peaks: 458 WARNING @ Sun, 21 Jun 2020 18:19:23: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Sun, 21 Jun 2020 18:19:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:24: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:19:24: #2 alternative fragment length(s) may be 1,32,585,597 bps INFO @ Sun, 21 Jun 2020 18:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.05_model.r WARNING @ Sun, 21 Jun 2020 18:19:24: #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 18:19:24: #2 You may need to consider one of the other alternative d(s): 1,32,585,597 WARNING @ Sun, 21 Jun 2020 18:19:24: #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 18:19:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:19:25: 20000000 INFO @ Sun, 21 Jun 2020 18:19:26: 26000000 INFO @ Sun, 21 Jun 2020 18:19:30: 21000000 INFO @ Sun, 21 Jun 2020 18:19:32: 27000000 INFO @ Sun, 21 Jun 2020 18:19:35: 22000000 INFO @ Sun, 21 Jun 2020 18:19:37: 28000000 INFO @ Sun, 21 Jun 2020 18:19:40: 23000000 INFO @ Sun, 21 Jun 2020 18:19:42: 29000000 INFO @ Sun, 21 Jun 2020 18:19:46: 24000000 INFO @ Sun, 21 Jun 2020 18:19:47: 30000000 INFO @ Sun, 21 Jun 2020 18:19:51: 25000000 INFO @ Sun, 21 Jun 2020 18:19:51: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:19:51: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:19:51: #1 total tags in treatment: 30666128 INFO @ Sun, 21 Jun 2020 18:19:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:19:52: #1 tags after filtering in treatment: 30666107 INFO @ Sun, 21 Jun 2020 18:19:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:54: #2 number of paired peaks: 458 WARNING @ Sun, 21 Jun 2020 18:19:54: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Sun, 21 Jun 2020 18:19:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:54: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:19:54: #2 alternative fragment length(s) may be 1,32,585,597 bps INFO @ Sun, 21 Jun 2020 18:19:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.10_model.r WARNING @ Sun, 21 Jun 2020 18:19:54: #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 18:19:54: #2 You may need to consider one of the other alternative d(s): 1,32,585,597 WARNING @ Sun, 21 Jun 2020 18:19:54: #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 18:19:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:19:56: 26000000 INFO @ Sun, 21 Jun 2020 18:20:01: 27000000 INFO @ Sun, 21 Jun 2020 18:20:06: 28000000 INFO @ Sun, 21 Jun 2020 18:20:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:12: 29000000 INFO @ Sun, 21 Jun 2020 18:20:17: 30000000 INFO @ Sun, 21 Jun 2020 18:20:20: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:20:20: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:20:20: #1 total tags in treatment: 30666128 INFO @ Sun, 21 Jun 2020 18:20:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:20: #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 18:20:21: #1 tags after filtering in treatment: 30666107 INFO @ Sun, 21 Jun 2020 18:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:23: #2 number of paired peaks: 458 WARNING @ Sun, 21 Jun 2020 18:20:23: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:23: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:20:23: #2 alternative fragment length(s) may be 1,32,585,597 bps INFO @ Sun, 21 Jun 2020 18:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.20_model.r WARNING @ Sun, 21 Jun 2020 18:20:23: #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 18:20:23: #2 You may need to consider one of the other alternative d(s): 1,32,585,597 WARNING @ Sun, 21 Jun 2020 18:20:23: #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 18:20:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.05_summits.bed INFO @ Sun, 21 Jun 2020 18:20:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:20:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX146994/SRX146994.20_summits.bed INFO @ Sun, 21 Jun 2020 18:21:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling