Job ID = 6454756 SRX = SRX2564141 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:28:59 prefetch.2.10.7: 1) Downloading 'SRR5259260'... 2020-06-21T09:28:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:35:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:35:24 prefetch.2.10.7: 1) 'SRR5259260' was downloaded successfully 2020-06-21T09:35:24 prefetch.2.10.7: 'SRR5259260' has 0 unresolved dependencies Read 42694133 spots for SRR5259260/SRR5259260.sra Written 42694133 spots for SRR5259260/SRR5259260.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: 00:15:23 42694133 reads; of these: 42694133 (100.00%) were unpaired; of these: 4814999 (11.28%) aligned 0 times 29773725 (69.74%) aligned exactly 1 time 8105409 (18.98%) aligned >1 times 88.72% overall alignment rate Time searching: 00:15:23 Overall time: 00:15:23 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 16 files... [bam_rmdupse_core] 5552135 / 37879134 = 0.1466 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 19:08:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.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 19:08:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:33: 1000000 INFO @ Sun, 21 Jun 2020 19:08:40: 2000000 INFO @ Sun, 21 Jun 2020 19:08:47: 3000000 INFO @ Sun, 21 Jun 2020 19:08:53: 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 19:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.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 19:08:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:00: 5000000 INFO @ Sun, 21 Jun 2020 19:09:05: 1000000 INFO @ Sun, 21 Jun 2020 19:09:07: 6000000 INFO @ Sun, 21 Jun 2020 19:09:12: 2000000 INFO @ Sun, 21 Jun 2020 19:09:14: 7000000 INFO @ Sun, 21 Jun 2020 19:09:19: 3000000 INFO @ Sun, 21 Jun 2020 19:09:21: 8000000 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 19:09:26: 4000000 INFO @ Sun, 21 Jun 2020 19:09:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.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 19:09:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:28: 9000000 INFO @ Sun, 21 Jun 2020 19:09:34: 5000000 INFO @ Sun, 21 Jun 2020 19:09:35: 1000000 INFO @ Sun, 21 Jun 2020 19:09:36: 10000000 INFO @ Sun, 21 Jun 2020 19:09:41: 6000000 INFO @ Sun, 21 Jun 2020 19:09:42: 2000000 INFO @ Sun, 21 Jun 2020 19:09:43: 11000000 INFO @ Sun, 21 Jun 2020 19:09:48: 7000000 INFO @ Sun, 21 Jun 2020 19:09:50: 3000000 INFO @ Sun, 21 Jun 2020 19:09:50: 12000000 INFO @ Sun, 21 Jun 2020 19:09:55: 8000000 INFO @ Sun, 21 Jun 2020 19:09:57: 13000000 INFO @ Sun, 21 Jun 2020 19:09:57: 4000000 INFO @ Sun, 21 Jun 2020 19:10:02: 9000000 INFO @ Sun, 21 Jun 2020 19:10:05: 5000000 INFO @ Sun, 21 Jun 2020 19:10:05: 14000000 INFO @ Sun, 21 Jun 2020 19:10:09: 10000000 INFO @ Sun, 21 Jun 2020 19:10:12: 6000000 INFO @ Sun, 21 Jun 2020 19:10:13: 15000000 INFO @ Sun, 21 Jun 2020 19:10:17: 11000000 INFO @ Sun, 21 Jun 2020 19:10:20: 7000000 INFO @ Sun, 21 Jun 2020 19:10:20: 16000000 INFO @ Sun, 21 Jun 2020 19:10:24: 12000000 INFO @ Sun, 21 Jun 2020 19:10:27: 8000000 INFO @ Sun, 21 Jun 2020 19:10:28: 17000000 INFO @ Sun, 21 Jun 2020 19:10:31: 13000000 INFO @ Sun, 21 Jun 2020 19:10:34: 9000000 INFO @ Sun, 21 Jun 2020 19:10:35: 18000000 INFO @ Sun, 21 Jun 2020 19:10:39: 14000000 INFO @ Sun, 21 Jun 2020 19:10:41: 10000000 INFO @ Sun, 21 Jun 2020 19:10:43: 19000000 INFO @ Sun, 21 Jun 2020 19:10:46: 15000000 INFO @ Sun, 21 Jun 2020 19:10:48: 11000000 INFO @ Sun, 21 Jun 2020 19:10:50: 20000000 INFO @ Sun, 21 Jun 2020 19:10:53: 16000000 INFO @ Sun, 21 Jun 2020 19:10:56: 12000000 INFO @ Sun, 21 Jun 2020 19:10:57: 21000000 INFO @ Sun, 21 Jun 2020 19:11:00: 17000000 INFO @ Sun, 21 Jun 2020 19:11:03: 13000000 INFO @ Sun, 21 Jun 2020 19:11:04: 22000000 INFO @ Sun, 21 Jun 2020 19:11:08: 18000000 INFO @ Sun, 21 Jun 2020 19:11:10: 14000000 INFO @ Sun, 21 Jun 2020 19:11:11: 23000000 INFO @ Sun, 21 Jun 2020 19:11:15: 19000000 INFO @ Sun, 21 Jun 2020 19:11:17: 15000000 INFO @ Sun, 21 Jun 2020 19:11:19: 24000000 INFO @ Sun, 21 Jun 2020 19:11:22: 20000000 INFO @ Sun, 21 Jun 2020 19:11:25: 16000000 INFO @ Sun, 21 Jun 2020 19:11:26: 25000000 INFO @ Sun, 21 Jun 2020 19:11:29: 21000000 INFO @ Sun, 21 Jun 2020 19:11:32: 17000000 INFO @ Sun, 21 Jun 2020 19:11:33: 26000000 INFO @ Sun, 21 Jun 2020 19:11:37: 22000000 INFO @ Sun, 21 Jun 2020 19:11:39: 18000000 INFO @ Sun, 21 Jun 2020 19:11:41: 27000000 INFO @ Sun, 21 Jun 2020 19:11:44: 23000000 INFO @ Sun, 21 Jun 2020 19:11:46: 19000000 INFO @ Sun, 21 Jun 2020 19:11:48: 28000000 INFO @ Sun, 21 Jun 2020 19:11:51: 24000000 INFO @ Sun, 21 Jun 2020 19:11:53: 20000000 INFO @ Sun, 21 Jun 2020 19:11:56: 29000000 INFO @ Sun, 21 Jun 2020 19:11:58: 25000000 INFO @ Sun, 21 Jun 2020 19:12:00: 21000000 INFO @ Sun, 21 Jun 2020 19:12:03: 30000000 INFO @ Sun, 21 Jun 2020 19:12:05: 26000000 INFO @ Sun, 21 Jun 2020 19:12:07: 22000000 INFO @ Sun, 21 Jun 2020 19:12:10: 31000000 INFO @ Sun, 21 Jun 2020 19:12:13: 27000000 INFO @ Sun, 21 Jun 2020 19:12:14: 23000000 INFO @ Sun, 21 Jun 2020 19:12:17: 32000000 INFO @ Sun, 21 Jun 2020 19:12:20: 28000000 INFO @ Sun, 21 Jun 2020 19:12:20: #1 tag size is determined as 71 bps INFO @ Sun, 21 Jun 2020 19:12:20: #1 tag size = 71 INFO @ Sun, 21 Jun 2020 19:12:20: #1 total tags in treatment: 32326999 INFO @ Sun, 21 Jun 2020 19:12:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:20: #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 19:12:21: #1 tags after filtering in treatment: 32326999 INFO @ Sun, 21 Jun 2020 19:12:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:21: 24000000 INFO @ Sun, 21 Jun 2020 19:12:23: #2 number of paired peaks: 161 WARNING @ Sun, 21 Jun 2020 19:12:23: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:23: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:12:23: #2 alternative fragment length(s) may be 2,29,576 bps INFO @ Sun, 21 Jun 2020 19:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.05_model.r WARNING @ Sun, 21 Jun 2020 19:12:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:23: #2 You may need to consider one of the other alternative d(s): 2,29,576 WARNING @ Sun, 21 Jun 2020 19:12:23: #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 19:12:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:27: 29000000 INFO @ Sun, 21 Jun 2020 19:12:28: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:12:34: 30000000 INFO @ Sun, 21 Jun 2020 19:12:35: 26000000 INFO @ Sun, 21 Jun 2020 19:12:40: 31000000 INFO @ Sun, 21 Jun 2020 19:12:42: 27000000 INFO @ Sun, 21 Jun 2020 19:12:48: 32000000 INFO @ Sun, 21 Jun 2020 19:12:49: 28000000 INFO @ Sun, 21 Jun 2020 19:12:50: #1 tag size is determined as 71 bps INFO @ Sun, 21 Jun 2020 19:12:50: #1 tag size = 71 INFO @ Sun, 21 Jun 2020 19:12:50: #1 total tags in treatment: 32326999 INFO @ Sun, 21 Jun 2020 19:12:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:50: #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 19:12:51: #1 tags after filtering in treatment: 32326999 INFO @ Sun, 21 Jun 2020 19:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:53: #2 number of paired peaks: 161 WARNING @ Sun, 21 Jun 2020 19:12:53: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:53: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:12:53: #2 alternative fragment length(s) may be 2,29,576 bps INFO @ Sun, 21 Jun 2020 19:12:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.10_model.r WARNING @ Sun, 21 Jun 2020 19:12:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:53: #2 You may need to consider one of the other alternative d(s): 2,29,576 WARNING @ Sun, 21 Jun 2020 19:12:53: #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 19:12:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:56: 29000000 INFO @ Sun, 21 Jun 2020 19:13:02: 30000000 INFO @ Sun, 21 Jun 2020 19:13:09: 31000000 INFO @ Sun, 21 Jun 2020 19:13:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:16: 32000000 INFO @ Sun, 21 Jun 2020 19:13:18: #1 tag size is determined as 71 bps INFO @ Sun, 21 Jun 2020 19:13:18: #1 tag size = 71 INFO @ Sun, 21 Jun 2020 19:13:18: #1 total tags in treatment: 32326999 INFO @ Sun, 21 Jun 2020 19:13:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:18: #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 19:13:19: #1 tags after filtering in treatment: 32326999 INFO @ Sun, 21 Jun 2020 19:13:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:21: #2 number of paired peaks: 161 WARNING @ Sun, 21 Jun 2020 19:13:21: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:21: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:13:21: #2 alternative fragment length(s) may be 2,29,576 bps INFO @ Sun, 21 Jun 2020 19:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.20_model.r WARNING @ Sun, 21 Jun 2020 19:13:21: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:21: #2 You may need to consider one of the other alternative d(s): 2,29,576 WARNING @ Sun, 21 Jun 2020 19:13:21: #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 19:13:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.05_summits.bed INFO @ Sun, 21 Jun 2020 19:13:35: 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 19:13:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.10_summits.bed INFO @ Sun, 21 Jun 2020 19:14:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564141/SRX2564141.20_summits.bed INFO @ Sun, 21 Jun 2020 19:14:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling