Job ID = 6456026 SRX = SRX3159483 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:47:23 prefetch.2.10.7: 1) Downloading 'SRR6004213'... 2020-06-21T10:47:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:52:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:52:13 prefetch.2.10.7: 1) 'SRR6004213' was downloaded successfully 2020-06-21T10:52:13 prefetch.2.10.7: 'SRR6004213' has 0 unresolved dependencies Read 61020936 spots for SRR6004213/SRR6004213.sra Written 61020936 spots for SRR6004213/SRR6004213.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: 00:19:01 61020936 reads; of these: 61020936 (100.00%) were unpaired; of these: 1623944 (2.66%) aligned 0 times 41849506 (68.58%) aligned exactly 1 time 17547486 (28.76%) aligned >1 times 97.34% overall alignment rate Time searching: 00:19:01 Overall time: 00:19:01 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 28 files... [bam_rmdupse_core] 18656519 / 59396992 = 0.3141 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 20:23:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.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 20:23:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:59: 1000000 INFO @ Sun, 21 Jun 2020 20:24:05: 2000000 INFO @ Sun, 21 Jun 2020 20:24:10: 3000000 INFO @ Sun, 21 Jun 2020 20:24:15: 4000000 INFO @ Sun, 21 Jun 2020 20:24:21: 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 20:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.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 20:24:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:27: 6000000 INFO @ Sun, 21 Jun 2020 20:24:30: 1000000 INFO @ Sun, 21 Jun 2020 20:24:33: 7000000 INFO @ Sun, 21 Jun 2020 20:24:36: 2000000 INFO @ Sun, 21 Jun 2020 20:24:39: 8000000 INFO @ Sun, 21 Jun 2020 20:24:42: 3000000 INFO @ Sun, 21 Jun 2020 20:24:45: 9000000 INFO @ Sun, 21 Jun 2020 20:24:48: 4000000 INFO @ Sun, 21 Jun 2020 20:24:50: 10000000 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 20:24:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.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 20:24:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:54: 5000000 INFO @ Sun, 21 Jun 2020 20:24:57: 11000000 INFO @ Sun, 21 Jun 2020 20:25:01: 6000000 INFO @ Sun, 21 Jun 2020 20:25:01: 1000000 INFO @ Sun, 21 Jun 2020 20:25:03: 12000000 INFO @ Sun, 21 Jun 2020 20:25:07: 7000000 INFO @ Sun, 21 Jun 2020 20:25:09: 2000000 INFO @ Sun, 21 Jun 2020 20:25:10: 13000000 INFO @ Sun, 21 Jun 2020 20:25:14: 8000000 INFO @ Sun, 21 Jun 2020 20:25:16: 3000000 INFO @ Sun, 21 Jun 2020 20:25:17: 14000000 INFO @ Sun, 21 Jun 2020 20:25:20: 9000000 INFO @ Sun, 21 Jun 2020 20:25:23: 4000000 INFO @ Sun, 21 Jun 2020 20:25:23: 15000000 INFO @ Sun, 21 Jun 2020 20:25:27: 10000000 INFO @ Sun, 21 Jun 2020 20:25:30: 16000000 INFO @ Sun, 21 Jun 2020 20:25:30: 5000000 INFO @ Sun, 21 Jun 2020 20:25:34: 11000000 INFO @ Sun, 21 Jun 2020 20:25:36: 17000000 INFO @ Sun, 21 Jun 2020 20:25:38: 6000000 INFO @ Sun, 21 Jun 2020 20:25:40: 12000000 INFO @ Sun, 21 Jun 2020 20:25:43: 18000000 INFO @ Sun, 21 Jun 2020 20:25:45: 7000000 INFO @ Sun, 21 Jun 2020 20:25:47: 13000000 INFO @ Sun, 21 Jun 2020 20:25:50: 19000000 INFO @ Sun, 21 Jun 2020 20:25:52: 8000000 INFO @ Sun, 21 Jun 2020 20:25:54: 14000000 INFO @ Sun, 21 Jun 2020 20:25:57: 20000000 INFO @ Sun, 21 Jun 2020 20:25:59: 9000000 INFO @ Sun, 21 Jun 2020 20:26:00: 15000000 INFO @ Sun, 21 Jun 2020 20:26:03: 21000000 INFO @ Sun, 21 Jun 2020 20:26:06: 10000000 INFO @ Sun, 21 Jun 2020 20:26:07: 16000000 INFO @ Sun, 21 Jun 2020 20:26:10: 22000000 INFO @ Sun, 21 Jun 2020 20:26:13: 11000000 INFO @ Sun, 21 Jun 2020 20:26:14: 17000000 INFO @ Sun, 21 Jun 2020 20:26:17: 23000000 INFO @ Sun, 21 Jun 2020 20:26:20: 12000000 INFO @ Sun, 21 Jun 2020 20:26:21: 18000000 INFO @ Sun, 21 Jun 2020 20:26:24: 24000000 INFO @ Sun, 21 Jun 2020 20:26:27: 13000000 INFO @ Sun, 21 Jun 2020 20:26:28: 19000000 INFO @ Sun, 21 Jun 2020 20:26:31: 25000000 INFO @ Sun, 21 Jun 2020 20:26:34: 14000000 INFO @ Sun, 21 Jun 2020 20:26:34: 20000000 INFO @ Sun, 21 Jun 2020 20:26:38: 26000000 INFO @ Sun, 21 Jun 2020 20:26:41: 15000000 INFO @ Sun, 21 Jun 2020 20:26:41: 21000000 INFO @ Sun, 21 Jun 2020 20:26:44: 27000000 INFO @ Sun, 21 Jun 2020 20:26:48: 22000000 INFO @ Sun, 21 Jun 2020 20:26:48: 16000000 INFO @ Sun, 21 Jun 2020 20:26:51: 28000000 INFO @ Sun, 21 Jun 2020 20:26:55: 23000000 INFO @ Sun, 21 Jun 2020 20:26:55: 17000000 INFO @ Sun, 21 Jun 2020 20:26:58: 29000000 INFO @ Sun, 21 Jun 2020 20:27:02: 24000000 INFO @ Sun, 21 Jun 2020 20:27:02: 18000000 INFO @ Sun, 21 Jun 2020 20:27:05: 30000000 INFO @ Sun, 21 Jun 2020 20:27:08: 25000000 INFO @ Sun, 21 Jun 2020 20:27:10: 19000000 INFO @ Sun, 21 Jun 2020 20:27:11: 31000000 INFO @ Sun, 21 Jun 2020 20:27:15: 26000000 INFO @ Sun, 21 Jun 2020 20:27:17: 20000000 INFO @ Sun, 21 Jun 2020 20:27:18: 32000000 INFO @ Sun, 21 Jun 2020 20:27:22: 27000000 INFO @ Sun, 21 Jun 2020 20:27:24: 21000000 INFO @ Sun, 21 Jun 2020 20:27:25: 33000000 INFO @ Sun, 21 Jun 2020 20:27:28: 28000000 INFO @ Sun, 21 Jun 2020 20:27:31: 22000000 INFO @ Sun, 21 Jun 2020 20:27:32: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:27:35: 29000000 INFO @ Sun, 21 Jun 2020 20:27:38: 23000000 INFO @ Sun, 21 Jun 2020 20:27:38: 35000000 INFO @ Sun, 21 Jun 2020 20:27:42: 30000000 INFO @ Sun, 21 Jun 2020 20:27:45: 24000000 INFO @ Sun, 21 Jun 2020 20:27:45: 36000000 INFO @ Sun, 21 Jun 2020 20:27:48: 31000000 INFO @ Sun, 21 Jun 2020 20:27:52: 37000000 INFO @ Sun, 21 Jun 2020 20:27:52: 25000000 INFO @ Sun, 21 Jun 2020 20:27:55: 32000000 INFO @ Sun, 21 Jun 2020 20:27:59: 38000000 INFO @ Sun, 21 Jun 2020 20:27:59: 26000000 INFO @ Sun, 21 Jun 2020 20:28:02: 33000000 INFO @ Sun, 21 Jun 2020 20:28:06: 39000000 INFO @ Sun, 21 Jun 2020 20:28:07: 27000000 INFO @ Sun, 21 Jun 2020 20:28:09: 34000000 INFO @ Sun, 21 Jun 2020 20:28:13: 40000000 INFO @ Sun, 21 Jun 2020 20:28:14: 28000000 INFO @ Sun, 21 Jun 2020 20:28:16: 35000000 INFO @ Sun, 21 Jun 2020 20:28:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:28:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:28:18: #1 total tags in treatment: 40740473 INFO @ Sun, 21 Jun 2020 20:28:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:18: #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 20:28:19: #1 tags after filtering in treatment: 40740463 INFO @ Sun, 21 Jun 2020 20:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:19: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:21: 29000000 INFO @ Sun, 21 Jun 2020 20:28:21: #2 number of paired peaks: 143 WARNING @ Sun, 21 Jun 2020 20:28:21: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:21: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:22: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:28:22: #2 alternative fragment length(s) may be 2,11,42,560 bps INFO @ Sun, 21 Jun 2020 20:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.05_model.r WARNING @ Sun, 21 Jun 2020 20:28:22: #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 20:28:22: #2 You may need to consider one of the other alternative d(s): 2,11,42,560 WARNING @ Sun, 21 Jun 2020 20:28:22: #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 20:28:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:23: 36000000 INFO @ Sun, 21 Jun 2020 20:28:28: 30000000 INFO @ Sun, 21 Jun 2020 20:28:29: 37000000 INFO @ Sun, 21 Jun 2020 20:28:36: 31000000 INFO @ Sun, 21 Jun 2020 20:28:36: 38000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:28:43: 39000000 INFO @ Sun, 21 Jun 2020 20:28:43: 32000000 INFO @ Sun, 21 Jun 2020 20:28:49: 40000000 INFO @ Sun, 21 Jun 2020 20:28:51: 33000000 INFO @ Sun, 21 Jun 2020 20:28:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:28:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:28:54: #1 total tags in treatment: 40740473 INFO @ Sun, 21 Jun 2020 20:28:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:54: #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 20:28:55: #1 tags after filtering in treatment: 40740463 INFO @ Sun, 21 Jun 2020 20:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:55: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:58: 34000000 INFO @ Sun, 21 Jun 2020 20:28:58: #2 number of paired peaks: 143 WARNING @ Sun, 21 Jun 2020 20:28:58: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:58: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:58: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:58: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:58: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:58: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:28:58: #2 alternative fragment length(s) may be 2,11,42,560 bps INFO @ Sun, 21 Jun 2020 20:28:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.10_model.r WARNING @ Sun, 21 Jun 2020 20:28:58: #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 20:28:58: #2 You may need to consider one of the other alternative d(s): 2,11,42,560 WARNING @ Sun, 21 Jun 2020 20:28:58: #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 20:28:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:04: 35000000 INFO @ Sun, 21 Jun 2020 20:29:10: 36000000 INFO @ Sun, 21 Jun 2020 20:29:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:17: 37000000 INFO @ Sun, 21 Jun 2020 20:29:23: 38000000 INFO @ Sun, 21 Jun 2020 20:29:30: 39000000 INFO @ Sun, 21 Jun 2020 20:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:36: 40000000 INFO @ Sun, 21 Jun 2020 20:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.05_summits.bed INFO @ Sun, 21 Jun 2020 20:29:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:29:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:41: #1 total tags in treatment: 40740473 INFO @ Sun, 21 Jun 2020 20:29:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:41: #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 20:29:42: #1 tags after filtering in treatment: 40740463 INFO @ Sun, 21 Jun 2020 20:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:44: #2 number of paired peaks: 143 WARNING @ Sun, 21 Jun 2020 20:29:44: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:44: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:44: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:44: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:44: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:29:44: #2 alternative fragment length(s) may be 2,11,42,560 bps INFO @ Sun, 21 Jun 2020 20:29:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.20_model.r WARNING @ Sun, 21 Jun 2020 20:29:44: #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 20:29:44: #2 You may need to consider one of the other alternative d(s): 2,11,42,560 WARNING @ Sun, 21 Jun 2020 20:29:44: #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 20:29:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.10_summits.bed INFO @ Sun, 21 Jun 2020 20:30:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:30:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159483/SRX3159483.20_summits.bed INFO @ Sun, 21 Jun 2020 20:31:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling