Job ID = 6458787 SRX = SRX5436060 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:58:16 prefetch.2.10.7: 1) Downloading 'SRR8637392'... 2020-06-21T12:58:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:04:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:04:30 prefetch.2.10.7: 1) 'SRR8637392' was downloaded successfully Read 46705183 spots for SRR8637392/SRR8637392.sra Written 46705183 spots for SRR8637392/SRR8637392.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: 00:13:16 46705183 reads; of these: 46705183 (100.00%) were unpaired; of these: 2378491 (5.09%) aligned 0 times 30884331 (66.13%) aligned exactly 1 time 13442361 (28.78%) aligned >1 times 94.91% overall alignment rate Time searching: 00:13:16 Overall time: 00:13:16 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] 9648528 / 44326692 = 0.2177 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 22:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.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 22:31:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:31:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:31:24: 1000000 INFO @ Sun, 21 Jun 2020 22:31:30: 2000000 INFO @ Sun, 21 Jun 2020 22:31:36: 3000000 INFO @ Sun, 21 Jun 2020 22:31:41: 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 22:31:47: 5000000 INFO @ Sun, 21 Jun 2020 22:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.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 22:31:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:31:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:31:53: 6000000 INFO @ Sun, 21 Jun 2020 22:31:54: 1000000 INFO @ Sun, 21 Jun 2020 22:31:59: 7000000 INFO @ Sun, 21 Jun 2020 22:32:01: 2000000 INFO @ Sun, 21 Jun 2020 22:32:05: 8000000 INFO @ Sun, 21 Jun 2020 22:32:07: 3000000 INFO @ Sun, 21 Jun 2020 22:32:11: 9000000 INFO @ Sun, 21 Jun 2020 22:32:13: 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 @ Sun, 21 Jun 2020 22:32:17: 10000000 INFO @ Sun, 21 Jun 2020 22:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.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 22:32:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:32:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:32:19: 5000000 INFO @ Sun, 21 Jun 2020 22:32:24: 11000000 INFO @ Sun, 21 Jun 2020 22:32:25: 1000000 INFO @ Sun, 21 Jun 2020 22:32:26: 6000000 INFO @ Sun, 21 Jun 2020 22:32:32: 7000000 INFO @ Sun, 21 Jun 2020 22:32:32: 12000000 INFO @ Sun, 21 Jun 2020 22:32:33: 2000000 INFO @ Sun, 21 Jun 2020 22:32:38: 8000000 INFO @ Sun, 21 Jun 2020 22:32:40: 13000000 INFO @ Sun, 21 Jun 2020 22:32:41: 3000000 INFO @ Sun, 21 Jun 2020 22:32:44: 9000000 INFO @ Sun, 21 Jun 2020 22:32:47: 14000000 INFO @ Sun, 21 Jun 2020 22:32:49: 4000000 INFO @ Sun, 21 Jun 2020 22:32:50: 10000000 INFO @ Sun, 21 Jun 2020 22:32:55: 15000000 INFO @ Sun, 21 Jun 2020 22:32:56: 5000000 INFO @ Sun, 21 Jun 2020 22:32:57: 11000000 INFO @ Sun, 21 Jun 2020 22:33:03: 12000000 INFO @ Sun, 21 Jun 2020 22:33:03: 16000000 INFO @ Sun, 21 Jun 2020 22:33:04: 6000000 INFO @ Sun, 21 Jun 2020 22:33:10: 13000000 INFO @ Sun, 21 Jun 2020 22:33:11: 17000000 INFO @ Sun, 21 Jun 2020 22:33:12: 7000000 INFO @ Sun, 21 Jun 2020 22:33:17: 14000000 INFO @ Sun, 21 Jun 2020 22:33:18: 18000000 INFO @ Sun, 21 Jun 2020 22:33:19: 8000000 INFO @ Sun, 21 Jun 2020 22:33:24: 15000000 INFO @ Sun, 21 Jun 2020 22:33:25: 19000000 INFO @ Sun, 21 Jun 2020 22:33:27: 9000000 INFO @ Sun, 21 Jun 2020 22:33:31: 16000000 INFO @ Sun, 21 Jun 2020 22:33:33: 20000000 INFO @ Sun, 21 Jun 2020 22:33:34: 10000000 INFO @ Sun, 21 Jun 2020 22:33:38: 17000000 INFO @ Sun, 21 Jun 2020 22:33:40: 21000000 INFO @ Sun, 21 Jun 2020 22:33:42: 11000000 INFO @ Sun, 21 Jun 2020 22:33:45: 18000000 INFO @ Sun, 21 Jun 2020 22:33:48: 22000000 INFO @ Sun, 21 Jun 2020 22:33:50: 12000000 INFO @ Sun, 21 Jun 2020 22:33:50: 19000000 INFO @ Sun, 21 Jun 2020 22:33:56: 20000000 INFO @ Sun, 21 Jun 2020 22:33:56: 23000000 INFO @ Sun, 21 Jun 2020 22:33:58: 13000000 INFO @ Sun, 21 Jun 2020 22:34:02: 21000000 INFO @ Sun, 21 Jun 2020 22:34:04: 24000000 INFO @ Sun, 21 Jun 2020 22:34:06: 14000000 INFO @ Sun, 21 Jun 2020 22:34:08: 22000000 INFO @ Sun, 21 Jun 2020 22:34:12: 25000000 INFO @ Sun, 21 Jun 2020 22:34:13: 15000000 INFO @ Sun, 21 Jun 2020 22:34:15: 23000000 INFO @ Sun, 21 Jun 2020 22:34:19: 26000000 INFO @ Sun, 21 Jun 2020 22:34:20: 16000000 INFO @ Sun, 21 Jun 2020 22:34:21: 24000000 INFO @ Sun, 21 Jun 2020 22:34:26: 27000000 INFO @ Sun, 21 Jun 2020 22:34:27: 17000000 INFO @ Sun, 21 Jun 2020 22:34:27: 25000000 INFO @ Sun, 21 Jun 2020 22:34:33: 26000000 INFO @ Sun, 21 Jun 2020 22:34:33: 28000000 INFO @ Sun, 21 Jun 2020 22:34:34: 18000000 INFO @ Sun, 21 Jun 2020 22:34:39: 27000000 INFO @ Sun, 21 Jun 2020 22:34:42: 19000000 INFO @ Sun, 21 Jun 2020 22:34:42: 29000000 INFO @ Sun, 21 Jun 2020 22:34:45: 28000000 INFO @ Sun, 21 Jun 2020 22:34:49: 20000000 INFO @ Sun, 21 Jun 2020 22:34:50: 30000000 INFO @ Sun, 21 Jun 2020 22:34:52: 29000000 INFO @ Sun, 21 Jun 2020 22:34:57: 21000000 INFO @ Sun, 21 Jun 2020 22:34:57: 31000000 INFO @ Sun, 21 Jun 2020 22:34:59: 30000000 INFO @ Sun, 21 Jun 2020 22:35:03: 22000000 INFO @ Sun, 21 Jun 2020 22:35:04: 32000000 INFO @ Sun, 21 Jun 2020 22:35:06: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:35:10: 23000000 INFO @ Sun, 21 Jun 2020 22:35:11: 33000000 INFO @ Sun, 21 Jun 2020 22:35:13: 32000000 INFO @ Sun, 21 Jun 2020 22:35:17: 24000000 INFO @ Sun, 21 Jun 2020 22:35:18: 34000000 INFO @ Sun, 21 Jun 2020 22:35:20: 33000000 INFO @ Sun, 21 Jun 2020 22:35:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:35:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:35:22: #1 total tags in treatment: 34678164 INFO @ Sun, 21 Jun 2020 22:35:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:35:22: #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 22:35:23: 25000000 INFO @ Sun, 21 Jun 2020 22:35:23: #1 tags after filtering in treatment: 34678109 INFO @ Sun, 21 Jun 2020 22:35:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:35:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:35:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:35:26: #2 number of paired peaks: 576 WARNING @ Sun, 21 Jun 2020 22:35:26: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sun, 21 Jun 2020 22:35:26: start model_add_line... INFO @ Sun, 21 Jun 2020 22:35:26: 34000000 INFO @ Sun, 21 Jun 2020 22:35:26: start X-correlation... INFO @ Sun, 21 Jun 2020 22:35:26: end of X-cor INFO @ Sun, 21 Jun 2020 22:35:26: #2 finished! INFO @ Sun, 21 Jun 2020 22:35:26: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:35:26: #2 alternative fragment length(s) may be 1,31,564,584 bps INFO @ Sun, 21 Jun 2020 22:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.05_model.r WARNING @ Sun, 21 Jun 2020 22:35:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:35:26: #2 You may need to consider one of the other alternative d(s): 1,31,564,584 WARNING @ Sun, 21 Jun 2020 22:35:26: #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 22:35:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:35:30: 26000000 INFO @ Sun, 21 Jun 2020 22:35:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:35:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:35:31: #1 total tags in treatment: 34678164 INFO @ Sun, 21 Jun 2020 22:35:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:35:31: #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 22:35:32: #1 tags after filtering in treatment: 34678109 INFO @ Sun, 21 Jun 2020 22:35:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:35:32: #1 finished! INFO @ Sun, 21 Jun 2020 22:35:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:35:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:35:34: #2 number of paired peaks: 576 WARNING @ Sun, 21 Jun 2020 22:35:34: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sun, 21 Jun 2020 22:35:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:35:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:35:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:35:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:35:34: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:35:34: #2 alternative fragment length(s) may be 1,31,564,584 bps INFO @ Sun, 21 Jun 2020 22:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.10_model.r WARNING @ Sun, 21 Jun 2020 22:35:34: #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 22:35:34: #2 You may need to consider one of the other alternative d(s): 1,31,564,584 WARNING @ Sun, 21 Jun 2020 22:35:34: #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 22:35:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:35:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:35:37: 27000000 INFO @ Sun, 21 Jun 2020 22:35:45: 28000000 INFO @ Sun, 21 Jun 2020 22:35:52: 29000000 INFO @ Sun, 21 Jun 2020 22:35:58: 30000000 INFO @ Sun, 21 Jun 2020 22:36:04: 31000000 INFO @ Sun, 21 Jun 2020 22:36:10: 32000000 INFO @ Sun, 21 Jun 2020 22:36:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:36:16: 33000000 INFO @ Sun, 21 Jun 2020 22:36:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:36:22: 34000000 INFO @ Sun, 21 Jun 2020 22:36:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:36:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:36:26: #1 total tags in treatment: 34678164 INFO @ Sun, 21 Jun 2020 22:36:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:36:26: #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 22:36:27: #1 tags after filtering in treatment: 34678109 INFO @ Sun, 21 Jun 2020 22:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:36:27: #1 finished! INFO @ Sun, 21 Jun 2020 22:36:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:36:30: #2 number of paired peaks: 576 WARNING @ Sun, 21 Jun 2020 22:36:30: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sun, 21 Jun 2020 22:36:30: start model_add_line... INFO @ Sun, 21 Jun 2020 22:36:30: start X-correlation... INFO @ Sun, 21 Jun 2020 22:36:30: end of X-cor INFO @ Sun, 21 Jun 2020 22:36:30: #2 finished! INFO @ Sun, 21 Jun 2020 22:36:30: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:36:30: #2 alternative fragment length(s) may be 1,31,564,584 bps INFO @ Sun, 21 Jun 2020 22:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.20_model.r WARNING @ Sun, 21 Jun 2020 22:36:30: #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 22:36:30: #2 You may need to consider one of the other alternative d(s): 1,31,564,584 WARNING @ Sun, 21 Jun 2020 22:36:30: #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 22:36:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:36:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:36:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:36:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.05_summits.bed INFO @ Sun, 21 Jun 2020 22:36:32: 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 22:36:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:36:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:36:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.10_summits.bed INFO @ Sun, 21 Jun 2020 22:36:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:37:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:37:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:37:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:37:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436060/SRX5436060.20_summits.bed INFO @ Sun, 21 Jun 2020 22:37:35: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling