Job ID = 6455155 SRX = SRX2804217 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:38:25 prefetch.2.10.7: 1) Downloading 'SRR5534645'... 2020-06-21T09:38:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:43:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:43:41 prefetch.2.10.7: 1) 'SRR5534645' was downloaded successfully 2020-06-21T09:43:41 prefetch.2.10.7: 'SRR5534645' has 0 unresolved dependencies Read 53543860 spots for SRR5534645/SRR5534645.sra Written 53543860 spots for SRR5534645/SRR5534645.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: 00:00:01 Multiseed full-index search: 00:17:15 53543860 reads; of these: 53543860 (100.00%) were unpaired; of these: 1696108 (3.17%) aligned 0 times 35368227 (66.05%) aligned exactly 1 time 16479525 (30.78%) aligned >1 times 96.83% overall alignment rate Time searching: 00:17:16 Overall time: 00:17:16 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 24 files... [bam_rmdupse_core] 11896557 / 51847752 = 0.2295 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 19:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.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 19:12:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:38: 1000000 INFO @ Sun, 21 Jun 2020 19:12:43: 2000000 INFO @ Sun, 21 Jun 2020 19:12:48: 3000000 INFO @ Sun, 21 Jun 2020 19:12:52: 4000000 INFO @ Sun, 21 Jun 2020 19:12:57: 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 19:13:02: 6000000 INFO @ Sun, 21 Jun 2020 19:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.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 19:13:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:07: 7000000 INFO @ Sun, 21 Jun 2020 19:13:08: 1000000 INFO @ Sun, 21 Jun 2020 19:13:12: 8000000 INFO @ Sun, 21 Jun 2020 19:13:13: 2000000 INFO @ Sun, 21 Jun 2020 19:13:17: 9000000 INFO @ Sun, 21 Jun 2020 19:13:18: 3000000 INFO @ Sun, 21 Jun 2020 19:13:22: 10000000 INFO @ Sun, 21 Jun 2020 19:13:23: 4000000 INFO @ Sun, 21 Jun 2020 19:13:27: 11000000 INFO @ Sun, 21 Jun 2020 19:13:28: 5000000 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 19:13:32: 12000000 INFO @ Sun, 21 Jun 2020 19:13:33: 6000000 INFO @ Sun, 21 Jun 2020 19:13:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.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 19:13:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:37: 13000000 INFO @ Sun, 21 Jun 2020 19:13:38: 7000000 INFO @ Sun, 21 Jun 2020 19:13:39: 1000000 INFO @ Sun, 21 Jun 2020 19:13:42: 14000000 INFO @ Sun, 21 Jun 2020 19:13:43: 8000000 INFO @ Sun, 21 Jun 2020 19:13:45: 2000000 INFO @ Sun, 21 Jun 2020 19:13:47: 15000000 INFO @ Sun, 21 Jun 2020 19:13:48: 9000000 INFO @ Sun, 21 Jun 2020 19:13:51: 3000000 INFO @ Sun, 21 Jun 2020 19:13:53: 16000000 INFO @ Sun, 21 Jun 2020 19:13:53: 10000000 INFO @ Sun, 21 Jun 2020 19:13:57: 4000000 INFO @ Sun, 21 Jun 2020 19:13:58: 17000000 INFO @ Sun, 21 Jun 2020 19:13:58: 11000000 INFO @ Sun, 21 Jun 2020 19:14:03: 5000000 INFO @ Sun, 21 Jun 2020 19:14:03: 18000000 INFO @ Sun, 21 Jun 2020 19:14:03: 12000000 INFO @ Sun, 21 Jun 2020 19:14:08: 19000000 INFO @ Sun, 21 Jun 2020 19:14:08: 13000000 INFO @ Sun, 21 Jun 2020 19:14:09: 6000000 INFO @ Sun, 21 Jun 2020 19:14:13: 20000000 INFO @ Sun, 21 Jun 2020 19:14:13: 14000000 INFO @ Sun, 21 Jun 2020 19:14:14: 7000000 INFO @ Sun, 21 Jun 2020 19:14:18: 21000000 INFO @ Sun, 21 Jun 2020 19:14:18: 15000000 INFO @ Sun, 21 Jun 2020 19:14:20: 8000000 INFO @ Sun, 21 Jun 2020 19:14:23: 22000000 INFO @ Sun, 21 Jun 2020 19:14:23: 16000000 INFO @ Sun, 21 Jun 2020 19:14:26: 9000000 INFO @ Sun, 21 Jun 2020 19:14:28: 23000000 INFO @ Sun, 21 Jun 2020 19:14:28: 17000000 INFO @ Sun, 21 Jun 2020 19:14:32: 10000000 INFO @ Sun, 21 Jun 2020 19:14:33: 24000000 INFO @ Sun, 21 Jun 2020 19:14:33: 18000000 INFO @ Sun, 21 Jun 2020 19:14:38: 25000000 INFO @ Sun, 21 Jun 2020 19:14:38: 11000000 INFO @ Sun, 21 Jun 2020 19:14:38: 19000000 INFO @ Sun, 21 Jun 2020 19:14:43: 26000000 INFO @ Sun, 21 Jun 2020 19:14:43: 20000000 INFO @ Sun, 21 Jun 2020 19:14:44: 12000000 INFO @ Sun, 21 Jun 2020 19:14:48: 27000000 INFO @ Sun, 21 Jun 2020 19:14:48: 21000000 INFO @ Sun, 21 Jun 2020 19:14:50: 13000000 INFO @ Sun, 21 Jun 2020 19:14:53: 28000000 INFO @ Sun, 21 Jun 2020 19:14:53: 22000000 INFO @ Sun, 21 Jun 2020 19:14:56: 14000000 INFO @ Sun, 21 Jun 2020 19:14:58: 29000000 INFO @ Sun, 21 Jun 2020 19:14:58: 23000000 INFO @ Sun, 21 Jun 2020 19:15:01: 15000000 INFO @ Sun, 21 Jun 2020 19:15:03: 30000000 INFO @ Sun, 21 Jun 2020 19:15:03: 24000000 INFO @ Sun, 21 Jun 2020 19:15:07: 16000000 INFO @ Sun, 21 Jun 2020 19:15:08: 31000000 INFO @ Sun, 21 Jun 2020 19:15:08: 25000000 INFO @ Sun, 21 Jun 2020 19:15:13: 32000000 INFO @ Sun, 21 Jun 2020 19:15:13: 26000000 INFO @ Sun, 21 Jun 2020 19:15:13: 17000000 INFO @ Sun, 21 Jun 2020 19:15:18: 27000000 INFO @ Sun, 21 Jun 2020 19:15:18: 33000000 INFO @ Sun, 21 Jun 2020 19:15:19: 18000000 INFO @ Sun, 21 Jun 2020 19:15:23: 28000000 INFO @ Sun, 21 Jun 2020 19:15:23: 34000000 INFO @ Sun, 21 Jun 2020 19:15:25: 19000000 INFO @ Sun, 21 Jun 2020 19:15:28: 29000000 INFO @ Sun, 21 Jun 2020 19:15:28: 35000000 INFO @ Sun, 21 Jun 2020 19:15:30: 20000000 INFO @ Sun, 21 Jun 2020 19:15:33: 30000000 INFO @ Sun, 21 Jun 2020 19:15:33: 36000000 INFO @ Sun, 21 Jun 2020 19:15:36: 21000000 INFO @ Sun, 21 Jun 2020 19:15:38: 31000000 INFO @ Sun, 21 Jun 2020 19:15:38: 37000000 INFO @ Sun, 21 Jun 2020 19:15:42: 22000000 INFO @ Sun, 21 Jun 2020 19:15:43: 32000000 INFO @ Sun, 21 Jun 2020 19:15:44: 38000000 INFO @ Sun, 21 Jun 2020 19:15:48: 23000000 INFO @ Sun, 21 Jun 2020 19:15:48: 33000000 INFO @ Sun, 21 Jun 2020 19:15:49: 39000000 INFO @ Sun, 21 Jun 2020 19:15:53: 34000000 INFO @ Sun, 21 Jun 2020 19:15:53: 24000000 INFO @ Sun, 21 Jun 2020 19:15:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:15:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:15:54: #1 total tags in treatment: 39951195 INFO @ Sun, 21 Jun 2020 19:15:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:54: #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 19:15:55: #1 tags after filtering in treatment: 39951195 INFO @ Sun, 21 Jun 2020 19:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:57: #2 number of paired peaks: 128 WARNING @ Sun, 21 Jun 2020 19:15:57: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:57: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:15:57: #2 alternative fragment length(s) may be 1,27,48 bps INFO @ Sun, 21 Jun 2020 19:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.05_model.r WARNING @ Sun, 21 Jun 2020 19:15:57: #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 19:15:57: #2 You may need to consider one of the other alternative d(s): 1,27,48 WARNING @ Sun, 21 Jun 2020 19:15:57: #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 19:15:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:58: 35000000 INFO @ Sun, 21 Jun 2020 19:15:59: 25000000 INFO @ Sun, 21 Jun 2020 19:16:04: 36000000 INFO @ Sun, 21 Jun 2020 19:16:05: 26000000 INFO @ Sun, 21 Jun 2020 19:16:09: 37000000 INFO @ Sun, 21 Jun 2020 19:16:11: 27000000 INFO @ Sun, 21 Jun 2020 19:16:14: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:16:17: 28000000 INFO @ Sun, 21 Jun 2020 19:16:19: 39000000 INFO @ Sun, 21 Jun 2020 19:16:23: 29000000 INFO @ Sun, 21 Jun 2020 19:16:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:16:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:16:25: #1 total tags in treatment: 39951195 INFO @ Sun, 21 Jun 2020 19:16:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:25: #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 19:16:26: #1 tags after filtering in treatment: 39951195 INFO @ Sun, 21 Jun 2020 19:16:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:28: #2 number of paired peaks: 128 WARNING @ Sun, 21 Jun 2020 19:16:28: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:28: 30000000 INFO @ Sun, 21 Jun 2020 19:16:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:28: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:16:28: #2 alternative fragment length(s) may be 1,27,48 bps INFO @ Sun, 21 Jun 2020 19:16:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.10_model.r WARNING @ Sun, 21 Jun 2020 19:16:28: #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 19:16:28: #2 You may need to consider one of the other alternative d(s): 1,27,48 WARNING @ Sun, 21 Jun 2020 19:16:28: #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 19:16:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:34: 31000000 INFO @ Sun, 21 Jun 2020 19:16:40: 32000000 INFO @ Sun, 21 Jun 2020 19:16:46: 33000000 INFO @ Sun, 21 Jun 2020 19:16:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:52: 34000000 INFO @ Sun, 21 Jun 2020 19:16:57: 35000000 INFO @ Sun, 21 Jun 2020 19:17:03: 36000000 INFO @ Sun, 21 Jun 2020 19:17:09: 37000000 INFO @ Sun, 21 Jun 2020 19:17:14: 38000000 INFO @ Sun, 21 Jun 2020 19:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.05_summits.bed INFO @ Sun, 21 Jun 2020 19:17:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:17:20: 39000000 INFO @ Sun, 21 Jun 2020 19:17:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:17:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:17:26: #1 total tags in treatment: 39951195 INFO @ Sun, 21 Jun 2020 19:17:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:26: #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 19:17:26: #1 tags after filtering in treatment: 39951195 INFO @ Sun, 21 Jun 2020 19:17:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:29: #2 number of paired peaks: 128 WARNING @ Sun, 21 Jun 2020 19:17:29: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:29: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:17:29: #2 alternative fragment length(s) may be 1,27,48 bps INFO @ Sun, 21 Jun 2020 19:17:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.20_model.r WARNING @ Sun, 21 Jun 2020 19:17:29: #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 19:17:29: #2 You may need to consider one of the other alternative d(s): 1,27,48 WARNING @ Sun, 21 Jun 2020 19:17:29: #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 19:17:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:17:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.10_summits.bed INFO @ Sun, 21 Jun 2020 19:17:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:18:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804217/SRX2804217.20_summits.bed INFO @ Sun, 21 Jun 2020 19:18:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling