Job ID = 6453291 SRX = SRX110800 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:21:32 prefetch.2.10.7: 1) Downloading 'SRR388382'... 2020-06-21T08:21:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:28 prefetch.2.10.7: 'SRR388382' is valid 2020-06-21T08:24:28 prefetch.2.10.7: 1) 'SRR388382' was downloaded successfully Read 39078625 spots for SRR388382/SRR388382.sra Written 39078625 spots for SRR388382/SRR388382.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: 00:13:31 39078625 reads; of these: 39078625 (100.00%) were unpaired; of these: 739679 (1.89%) aligned 0 times 16860906 (43.15%) aligned exactly 1 time 21478040 (54.96%) aligned >1 times 98.11% overall alignment rate Time searching: 00:13:31 Overall time: 00:13:31 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 12 files... [bam_rmdupse_core] 10866346 / 38338946 = 0.2834 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 17:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.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 17:46:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:14: 1000000 INFO @ Sun, 21 Jun 2020 17:46:18: 2000000 INFO @ Sun, 21 Jun 2020 17:46:23: 3000000 INFO @ Sun, 21 Jun 2020 17:46:27: 4000000 INFO @ Sun, 21 Jun 2020 17:46:32: 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 17:46:37: 6000000 INFO @ Sun, 21 Jun 2020 17:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.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 17:46:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:41: 7000000 INFO @ Sun, 21 Jun 2020 17:46:43: 1000000 INFO @ Sun, 21 Jun 2020 17:46:46: 8000000 INFO @ Sun, 21 Jun 2020 17:46:48: 2000000 INFO @ Sun, 21 Jun 2020 17:46:50: 9000000 INFO @ Sun, 21 Jun 2020 17:46:53: 3000000 INFO @ Sun, 21 Jun 2020 17:46:55: 10000000 INFO @ Sun, 21 Jun 2020 17:46:58: 4000000 INFO @ Sun, 21 Jun 2020 17:46:59: 11000000 INFO @ Sun, 21 Jun 2020 17:47:03: 5000000 INFO @ Sun, 21 Jun 2020 17:47:04: 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 @ Sun, 21 Jun 2020 17:47:08: 6000000 INFO @ Sun, 21 Jun 2020 17:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.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 17:47:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:08: 13000000 INFO @ Sun, 21 Jun 2020 17:47:13: 7000000 INFO @ Sun, 21 Jun 2020 17:47:13: 14000000 INFO @ Sun, 21 Jun 2020 17:47:13: 1000000 INFO @ Sun, 21 Jun 2020 17:47:18: 8000000 INFO @ Sun, 21 Jun 2020 17:47:18: 15000000 INFO @ Sun, 21 Jun 2020 17:47:18: 2000000 INFO @ Sun, 21 Jun 2020 17:47:22: 16000000 INFO @ Sun, 21 Jun 2020 17:47:22: 9000000 INFO @ Sun, 21 Jun 2020 17:47:23: 3000000 INFO @ Sun, 21 Jun 2020 17:47:27: 17000000 INFO @ Sun, 21 Jun 2020 17:47:27: 10000000 INFO @ Sun, 21 Jun 2020 17:47:27: 4000000 INFO @ Sun, 21 Jun 2020 17:47:31: 18000000 INFO @ Sun, 21 Jun 2020 17:47:32: 11000000 INFO @ Sun, 21 Jun 2020 17:47:32: 5000000 INFO @ Sun, 21 Jun 2020 17:47:36: 19000000 INFO @ Sun, 21 Jun 2020 17:47:37: 12000000 INFO @ Sun, 21 Jun 2020 17:47:37: 6000000 INFO @ Sun, 21 Jun 2020 17:47:40: 20000000 INFO @ Sun, 21 Jun 2020 17:47:41: 13000000 INFO @ Sun, 21 Jun 2020 17:47:42: 7000000 INFO @ Sun, 21 Jun 2020 17:47:45: 21000000 INFO @ Sun, 21 Jun 2020 17:47:46: 14000000 INFO @ Sun, 21 Jun 2020 17:47:46: 8000000 INFO @ Sun, 21 Jun 2020 17:47:49: 22000000 INFO @ Sun, 21 Jun 2020 17:47:51: 9000000 INFO @ Sun, 21 Jun 2020 17:47:51: 15000000 INFO @ Sun, 21 Jun 2020 17:47:54: 23000000 INFO @ Sun, 21 Jun 2020 17:47:56: 10000000 INFO @ Sun, 21 Jun 2020 17:47:56: 16000000 INFO @ Sun, 21 Jun 2020 17:47:58: 24000000 INFO @ Sun, 21 Jun 2020 17:48:01: 11000000 INFO @ Sun, 21 Jun 2020 17:48:01: 17000000 INFO @ Sun, 21 Jun 2020 17:48:03: 25000000 INFO @ Sun, 21 Jun 2020 17:48:05: 12000000 INFO @ Sun, 21 Jun 2020 17:48:06: 18000000 INFO @ Sun, 21 Jun 2020 17:48:08: 26000000 INFO @ Sun, 21 Jun 2020 17:48:10: 13000000 INFO @ Sun, 21 Jun 2020 17:48:11: 19000000 INFO @ Sun, 21 Jun 2020 17:48:12: 27000000 INFO @ Sun, 21 Jun 2020 17:48:15: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:48:15: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:48:15: #1 total tags in treatment: 27472600 INFO @ Sun, 21 Jun 2020 17:48:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:15: #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 17:48:15: #1 tags after filtering in treatment: 27472600 INFO @ Sun, 21 Jun 2020 17:48:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:15: 14000000 INFO @ Sun, 21 Jun 2020 17:48:16: 20000000 INFO @ Sun, 21 Jun 2020 17:48:17: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 17:48:17: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:17: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:48:17: #2 alternative fragment length(s) may be 1,14 bps INFO @ Sun, 21 Jun 2020 17:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.05_model.r WARNING @ Sun, 21 Jun 2020 17:48:17: #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 17:48:17: #2 You may need to consider one of the other alternative d(s): 1,14 WARNING @ Sun, 21 Jun 2020 17:48:17: #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 17:48:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:20: 15000000 INFO @ Sun, 21 Jun 2020 17:48:21: 21000000 INFO @ Sun, 21 Jun 2020 17:48:25: 16000000 INFO @ Sun, 21 Jun 2020 17:48:26: 22000000 INFO @ Sun, 21 Jun 2020 17:48:30: 17000000 INFO @ Sun, 21 Jun 2020 17:48:31: 23000000 INFO @ Sun, 21 Jun 2020 17:48:35: 18000000 INFO @ Sun, 21 Jun 2020 17:48:36: 24000000 INFO @ Sun, 21 Jun 2020 17:48:39: 19000000 INFO @ Sun, 21 Jun 2020 17:48:41: 25000000 INFO @ Sun, 21 Jun 2020 17:48:44: 20000000 INFO @ Sun, 21 Jun 2020 17:48:46: 26000000 INFO @ Sun, 21 Jun 2020 17:48:49: 21000000 INFO @ Sun, 21 Jun 2020 17:48:51: 27000000 INFO @ Sun, 21 Jun 2020 17:48:53: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:48:53: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:48:53: #1 total tags in treatment: 27472600 INFO @ Sun, 21 Jun 2020 17:48:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:53: #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 17:48:54: #1 tags after filtering in treatment: 27472600 INFO @ Sun, 21 Jun 2020 17:48:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:54: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:54: 22000000 INFO @ Sun, 21 Jun 2020 17:48:56: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 17:48:56: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:56: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:48:56: #2 alternative fragment length(s) may be 1,14 bps INFO @ Sun, 21 Jun 2020 17:48:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.10_model.r WARNING @ Sun, 21 Jun 2020 17:48:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:48:56: #2 You may need to consider one of the other alternative d(s): 1,14 WARNING @ Sun, 21 Jun 2020 17:48:56: #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 17:48:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:59: 23000000 INFO @ Sun, 21 Jun 2020 17:49:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:03: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:49:08: 25000000 INFO @ Sun, 21 Jun 2020 17:49:13: 26000000 INFO @ Sun, 21 Jun 2020 17:49:18: 27000000 INFO @ Sun, 21 Jun 2020 17:49:20: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:49:20: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:49:20: #1 total tags in treatment: 27472600 INFO @ Sun, 21 Jun 2020 17:49:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:20: #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 17:49:21: #1 tags after filtering in treatment: 27472600 INFO @ Sun, 21 Jun 2020 17:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:23: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 17:49:23: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 17:49:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:23: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:49:23: #2 alternative fragment length(s) may be 1,14 bps INFO @ Sun, 21 Jun 2020 17:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.20_model.r WARNING @ Sun, 21 Jun 2020 17:49:23: #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 17:49:23: #2 You may need to consider one of the other alternative d(s): 1,14 WARNING @ Sun, 21 Jun 2020 17:49:23: #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 17:49:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.10_summits.bed INFO @ Sun, 21 Jun 2020 17:50:00: 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 17:50:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110800/SRX110800.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:29: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling