Job ID = 6528376 SRX = SRX5436051 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:55:28 prefetch.2.10.7: 1) Downloading 'SRR8637383'... 2020-06-29T14:55:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:59:35 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:59:35 prefetch.2.10.7: 1) 'SRR8637383' was downloaded successfully Read 43826563 spots for SRR8637383/SRR8637383.sra Written 43826563 spots for SRR8637383/SRR8637383.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: 00:12:36 43826563 reads; of these: 43826563 (100.00%) were unpaired; of these: 1683370 (3.84%) aligned 0 times 31133539 (71.04%) aligned exactly 1 time 11009654 (25.12%) aligned >1 times 96.16% overall alignment rate Time searching: 00:12:36 Overall time: 00:12:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 6865850 / 42143193 = 0.1629 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 @ Tue, 30 Jun 2020 00:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.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 @ Tue, 30 Jun 2020 00:32:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:32:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:32:07: 1000000 INFO @ Tue, 30 Jun 2020 00:32:11: 2000000 INFO @ Tue, 30 Jun 2020 00:32:16: 3000000 INFO @ Tue, 30 Jun 2020 00:32:21: 4000000 INFO @ Tue, 30 Jun 2020 00:32:25: 5000000 INFO @ Tue, 30 Jun 2020 00:32:30: 6000000 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 @ Tue, 30 Jun 2020 00:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.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 @ Tue, 30 Jun 2020 00:32:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:32:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:32:35: 7000000 INFO @ Tue, 30 Jun 2020 00:32:37: 1000000 INFO @ Tue, 30 Jun 2020 00:32:40: 8000000 INFO @ Tue, 30 Jun 2020 00:32:42: 2000000 INFO @ Tue, 30 Jun 2020 00:32:44: 9000000 INFO @ Tue, 30 Jun 2020 00:32:47: 3000000 INFO @ Tue, 30 Jun 2020 00:32:49: 10000000 INFO @ Tue, 30 Jun 2020 00:32:52: 4000000 INFO @ Tue, 30 Jun 2020 00:32:54: 11000000 INFO @ Tue, 30 Jun 2020 00:32:56: 5000000 INFO @ Tue, 30 Jun 2020 00:32:59: 12000000 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 @ Tue, 30 Jun 2020 00:33:01: 6000000 INFO @ Tue, 30 Jun 2020 00:33:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.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 @ Tue, 30 Jun 2020 00:33:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:33:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:33:04: 13000000 INFO @ Tue, 30 Jun 2020 00:33:06: 7000000 INFO @ Tue, 30 Jun 2020 00:33:07: 1000000 INFO @ Tue, 30 Jun 2020 00:33:09: 14000000 INFO @ Tue, 30 Jun 2020 00:33:11: 8000000 INFO @ Tue, 30 Jun 2020 00:33:12: 2000000 INFO @ Tue, 30 Jun 2020 00:33:14: 15000000 INFO @ Tue, 30 Jun 2020 00:33:16: 9000000 INFO @ Tue, 30 Jun 2020 00:33:17: 3000000 INFO @ Tue, 30 Jun 2020 00:33:19: 16000000 INFO @ Tue, 30 Jun 2020 00:33:21: 10000000 INFO @ Tue, 30 Jun 2020 00:33:22: 4000000 INFO @ Tue, 30 Jun 2020 00:33:24: 17000000 INFO @ Tue, 30 Jun 2020 00:33:26: 11000000 INFO @ Tue, 30 Jun 2020 00:33:27: 5000000 INFO @ Tue, 30 Jun 2020 00:33:28: 18000000 INFO @ Tue, 30 Jun 2020 00:33:31: 12000000 INFO @ Tue, 30 Jun 2020 00:33:32: 6000000 INFO @ Tue, 30 Jun 2020 00:33:33: 19000000 INFO @ Tue, 30 Jun 2020 00:33:36: 13000000 INFO @ Tue, 30 Jun 2020 00:33:37: 7000000 INFO @ Tue, 30 Jun 2020 00:33:38: 20000000 INFO @ Tue, 30 Jun 2020 00:33:40: 14000000 INFO @ Tue, 30 Jun 2020 00:33:42: 8000000 INFO @ Tue, 30 Jun 2020 00:33:43: 21000000 INFO @ Tue, 30 Jun 2020 00:33:45: 15000000 INFO @ Tue, 30 Jun 2020 00:33:47: 9000000 INFO @ Tue, 30 Jun 2020 00:33:48: 22000000 INFO @ Tue, 30 Jun 2020 00:33:50: 16000000 INFO @ Tue, 30 Jun 2020 00:33:52: 10000000 INFO @ Tue, 30 Jun 2020 00:33:53: 23000000 INFO @ Tue, 30 Jun 2020 00:33:55: 17000000 INFO @ Tue, 30 Jun 2020 00:33:57: 11000000 INFO @ Tue, 30 Jun 2020 00:33:58: 24000000 INFO @ Tue, 30 Jun 2020 00:34:00: 18000000 INFO @ Tue, 30 Jun 2020 00:34:02: 12000000 INFO @ Tue, 30 Jun 2020 00:34:03: 25000000 INFO @ Tue, 30 Jun 2020 00:34:05: 19000000 INFO @ Tue, 30 Jun 2020 00:34:07: 13000000 INFO @ Tue, 30 Jun 2020 00:34:08: 26000000 INFO @ Tue, 30 Jun 2020 00:34:10: 20000000 INFO @ Tue, 30 Jun 2020 00:34:12: 14000000 INFO @ Tue, 30 Jun 2020 00:34:13: 27000000 INFO @ Tue, 30 Jun 2020 00:34:15: 21000000 INFO @ Tue, 30 Jun 2020 00:34:17: 15000000 INFO @ Tue, 30 Jun 2020 00:34:17: 28000000 INFO @ Tue, 30 Jun 2020 00:34:20: 22000000 INFO @ Tue, 30 Jun 2020 00:34:22: 16000000 INFO @ Tue, 30 Jun 2020 00:34:22: 29000000 INFO @ Tue, 30 Jun 2020 00:34:25: 23000000 INFO @ Tue, 30 Jun 2020 00:34:27: 17000000 INFO @ Tue, 30 Jun 2020 00:34:27: 30000000 INFO @ Tue, 30 Jun 2020 00:34:29: 24000000 INFO @ Tue, 30 Jun 2020 00:34:32: 18000000 INFO @ Tue, 30 Jun 2020 00:34:32: 31000000 INFO @ Tue, 30 Jun 2020 00:34:34: 25000000 INFO @ Tue, 30 Jun 2020 00:34:37: 19000000 INFO @ Tue, 30 Jun 2020 00:34:37: 32000000 INFO @ Tue, 30 Jun 2020 00:34:39: 26000000 INFO @ Tue, 30 Jun 2020 00:34:42: 20000000 INFO @ Tue, 30 Jun 2020 00:34:42: 33000000 INFO @ Tue, 30 Jun 2020 00:34:44: 27000000 INFO @ Tue, 30 Jun 2020 00:34:47: 34000000 INFO @ Tue, 30 Jun 2020 00:34:47: 21000000 INFO @ Tue, 30 Jun 2020 00:34:49: 28000000 INFO @ Tue, 30 Jun 2020 00:34:52: 35000000 INFO @ Tue, 30 Jun 2020 00:34:52: 22000000 INFO @ Tue, 30 Jun 2020 00:34:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:34:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:34:53: #1 total tags in treatment: 35277343 INFO @ Tue, 30 Jun 2020 00:34:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:34:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:34:54: #1 tags after filtering in treatment: 35277343 INFO @ Tue, 30 Jun 2020 00:34:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:34:54: #1 finished! INFO @ Tue, 30 Jun 2020 00:34:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:34:54: 29000000 INFO @ Tue, 30 Jun 2020 00:34:56: #2 number of paired peaks: 216 WARNING @ Tue, 30 Jun 2020 00:34:56: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 30 Jun 2020 00:34:56: start model_add_line... INFO @ Tue, 30 Jun 2020 00:34:56: start X-correlation... INFO @ Tue, 30 Jun 2020 00:34:56: end of X-cor INFO @ Tue, 30 Jun 2020 00:34:56: #2 finished! INFO @ Tue, 30 Jun 2020 00:34:56: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:34:56: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 30 Jun 2020 00:34:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.05_model.r WARNING @ Tue, 30 Jun 2020 00:34:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:34:56: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 30 Jun 2020 00:34:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:34:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:34:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:34:57: 23000000 INFO @ Tue, 30 Jun 2020 00:34:59: 30000000 INFO @ Tue, 30 Jun 2020 00:35:02: 24000000 INFO @ Tue, 30 Jun 2020 00:35:04: 31000000 INFO @ Tue, 30 Jun 2020 00:35:07: 25000000 INFO @ Tue, 30 Jun 2020 00:35:09: 32000000 INFO @ Tue, 30 Jun 2020 00:35:12: 26000000 INFO @ Tue, 30 Jun 2020 00:35:14: 33000000 INFO @ Tue, 30 Jun 2020 00:35:17: 27000000 INFO @ Tue, 30 Jun 2020 00:35:19: 34000000 INFO @ Tue, 30 Jun 2020 00:35:22: 28000000 INFO @ Tue, 30 Jun 2020 00:35:23: 35000000 INFO @ Tue, 30 Jun 2020 00:35:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:35:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:35:25: #1 total tags in treatment: 35277343 INFO @ Tue, 30 Jun 2020 00:35:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:35:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:35:26: #1 tags after filtering in treatment: 35277343 INFO @ Tue, 30 Jun 2020 00:35:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:35:26: #1 finished! INFO @ Tue, 30 Jun 2020 00:35:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:35:27: 29000000 INFO @ Tue, 30 Jun 2020 00:35:28: #2 number of paired peaks: 216 WARNING @ Tue, 30 Jun 2020 00:35:28: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 30 Jun 2020 00:35:28: start model_add_line... INFO @ Tue, 30 Jun 2020 00:35:28: start X-correlation... INFO @ Tue, 30 Jun 2020 00:35:28: end of X-cor INFO @ Tue, 30 Jun 2020 00:35:28: #2 finished! INFO @ Tue, 30 Jun 2020 00:35:28: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:35:28: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 30 Jun 2020 00:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.10_model.r WARNING @ Tue, 30 Jun 2020 00:35:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:35:28: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 30 Jun 2020 00:35:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:35:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:35:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:35:32: 30000000 INFO @ Tue, 30 Jun 2020 00:35:37: 31000000 INFO @ Tue, 30 Jun 2020 00:35:42: 32000000 INFO @ Tue, 30 Jun 2020 00:35:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:35:47: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:35:52: 34000000 INFO @ Tue, 30 Jun 2020 00:35:56: 35000000 INFO @ Tue, 30 Jun 2020 00:35:58: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:35:58: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:35:58: #1 total tags in treatment: 35277343 INFO @ Tue, 30 Jun 2020 00:35:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:35:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:35:58: #1 tags after filtering in treatment: 35277343 INFO @ Tue, 30 Jun 2020 00:35:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:35:58: #1 finished! INFO @ Tue, 30 Jun 2020 00:35:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:35:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:36:01: #2 number of paired peaks: 216 WARNING @ Tue, 30 Jun 2020 00:36:01: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 30 Jun 2020 00:36:01: start model_add_line... INFO @ Tue, 30 Jun 2020 00:36:01: start X-correlation... INFO @ Tue, 30 Jun 2020 00:36:01: end of X-cor INFO @ Tue, 30 Jun 2020 00:36:01: #2 finished! INFO @ Tue, 30 Jun 2020 00:36:01: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:36:01: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 30 Jun 2020 00:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.20_model.r WARNING @ Tue, 30 Jun 2020 00:36:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:36:01: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 30 Jun 2020 00:36:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:36:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.05_summits.bed INFO @ Tue, 30 Jun 2020 00:36:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:36:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:36:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.10_summits.bed INFO @ Tue, 30 Jun 2020 00:36:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:36:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:37:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:37:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:37:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436051/SRX5436051.20_summits.bed INFO @ Tue, 30 Jun 2020 00:37:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling