Job ID = 6457501 SRX = SRX4664655 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:00:33 prefetch.2.10.7: 1) Downloading 'SRR7813082'... 2020-06-21T12:00:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:05:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:05:49 prefetch.2.10.7: 1) 'SRR7813082' was downloaded successfully Read 32361505 spots for SRR7813082/SRR7813082.sra Written 32361505 spots for SRR7813082/SRR7813082.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: 00:09:55 32361505 reads; of these: 32361505 (100.00%) were unpaired; of these: 812694 (2.51%) aligned 0 times 22679832 (70.08%) aligned exactly 1 time 8868979 (27.41%) aligned >1 times 97.49% overall alignment rate Time searching: 00:09:55 Overall time: 00:09:55 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] 4764761 / 31548811 = 0.1510 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 21:24:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.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 21:24:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:18: 1000000 INFO @ Sun, 21 Jun 2020 21:24:25: 2000000 INFO @ Sun, 21 Jun 2020 21:24:33: 3000000 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 21:24:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.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 21:24:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:40: 4000000 INFO @ Sun, 21 Jun 2020 21:24:49: 5000000 INFO @ Sun, 21 Jun 2020 21:24:49: 1000000 INFO @ Sun, 21 Jun 2020 21:24:57: 6000000 INFO @ Sun, 21 Jun 2020 21:24:57: 2000000 INFO @ Sun, 21 Jun 2020 21:25:05: 7000000 INFO @ Sun, 21 Jun 2020 21:25:06: 3000000 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 21:25:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.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 21:25:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:14: 4000000 INFO @ Sun, 21 Jun 2020 21:25:14: 8000000 INFO @ Sun, 21 Jun 2020 21:25:19: 1000000 INFO @ Sun, 21 Jun 2020 21:25:22: 5000000 INFO @ Sun, 21 Jun 2020 21:25:23: 9000000 INFO @ Sun, 21 Jun 2020 21:25:28: 2000000 INFO @ Sun, 21 Jun 2020 21:25:31: 6000000 INFO @ Sun, 21 Jun 2020 21:25:32: 10000000 INFO @ Sun, 21 Jun 2020 21:25:37: 3000000 INFO @ Sun, 21 Jun 2020 21:25:40: 7000000 INFO @ Sun, 21 Jun 2020 21:25:41: 11000000 INFO @ Sun, 21 Jun 2020 21:25:45: 4000000 INFO @ Sun, 21 Jun 2020 21:25:49: 8000000 INFO @ Sun, 21 Jun 2020 21:25:50: 12000000 INFO @ Sun, 21 Jun 2020 21:25:54: 5000000 INFO @ Sun, 21 Jun 2020 21:25:58: 9000000 INFO @ Sun, 21 Jun 2020 21:25:59: 13000000 INFO @ Sun, 21 Jun 2020 21:26:03: 6000000 INFO @ Sun, 21 Jun 2020 21:26:08: 10000000 INFO @ Sun, 21 Jun 2020 21:26:09: 14000000 INFO @ Sun, 21 Jun 2020 21:26:12: 7000000 INFO @ Sun, 21 Jun 2020 21:26:17: 11000000 INFO @ Sun, 21 Jun 2020 21:26:17: 15000000 INFO @ Sun, 21 Jun 2020 21:26:22: 8000000 INFO @ Sun, 21 Jun 2020 21:26:26: 12000000 INFO @ Sun, 21 Jun 2020 21:26:26: 16000000 INFO @ Sun, 21 Jun 2020 21:26:31: 9000000 INFO @ Sun, 21 Jun 2020 21:26:35: 13000000 INFO @ Sun, 21 Jun 2020 21:26:36: 17000000 INFO @ Sun, 21 Jun 2020 21:26:40: 10000000 INFO @ Sun, 21 Jun 2020 21:26:45: 14000000 INFO @ Sun, 21 Jun 2020 21:26:46: 18000000 INFO @ Sun, 21 Jun 2020 21:26:50: 11000000 INFO @ Sun, 21 Jun 2020 21:26:55: 15000000 INFO @ Sun, 21 Jun 2020 21:26:55: 19000000 INFO @ Sun, 21 Jun 2020 21:26:58: 12000000 INFO @ Sun, 21 Jun 2020 21:27:04: 16000000 INFO @ Sun, 21 Jun 2020 21:27:05: 20000000 INFO @ Sun, 21 Jun 2020 21:27:07: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:27:14: 17000000 INFO @ Sun, 21 Jun 2020 21:27:14: 21000000 INFO @ Sun, 21 Jun 2020 21:27:16: 14000000 INFO @ Sun, 21 Jun 2020 21:27:23: 18000000 INFO @ Sun, 21 Jun 2020 21:27:24: 22000000 INFO @ Sun, 21 Jun 2020 21:27:24: 15000000 INFO @ Sun, 21 Jun 2020 21:27:33: 16000000 INFO @ Sun, 21 Jun 2020 21:27:33: 19000000 INFO @ Sun, 21 Jun 2020 21:27:34: 23000000 INFO @ Sun, 21 Jun 2020 21:27:41: 17000000 INFO @ Sun, 21 Jun 2020 21:27:43: 20000000 INFO @ Sun, 21 Jun 2020 21:27:43: 24000000 INFO @ Sun, 21 Jun 2020 21:27:50: 18000000 INFO @ Sun, 21 Jun 2020 21:27:52: 21000000 INFO @ Sun, 21 Jun 2020 21:27:53: 25000000 INFO @ Sun, 21 Jun 2020 21:27:59: 19000000 INFO @ Sun, 21 Jun 2020 21:28:02: 22000000 INFO @ Sun, 21 Jun 2020 21:28:03: 26000000 INFO @ Sun, 21 Jun 2020 21:28:08: 20000000 INFO @ Sun, 21 Jun 2020 21:28:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:10: #1 total tags in treatment: 26784050 INFO @ Sun, 21 Jun 2020 21:28:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:10: #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 21:28:11: #1 tags after filtering in treatment: 26783993 INFO @ Sun, 21 Jun 2020 21:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:12: 23000000 INFO @ Sun, 21 Jun 2020 21:28:13: #2 number of paired peaks: 647 WARNING @ Sun, 21 Jun 2020 21:28:13: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sun, 21 Jun 2020 21:28:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:13: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:28:13: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 21:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.05_model.r WARNING @ Sun, 21 Jun 2020 21:28:13: #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 21:28:13: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 21:28:13: #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 21:28:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:16: 21000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:28:20: 24000000 INFO @ Sun, 21 Jun 2020 21:28:25: 22000000 INFO @ Sun, 21 Jun 2020 21:28:29: 25000000 INFO @ Sun, 21 Jun 2020 21:28:34: 23000000 INFO @ Sun, 21 Jun 2020 21:28:37: 26000000 INFO @ Sun, 21 Jun 2020 21:28:43: 24000000 INFO @ Sun, 21 Jun 2020 21:28:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:44: #1 total tags in treatment: 26784050 INFO @ Sun, 21 Jun 2020 21:28:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:44: #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 21:28:45: #1 tags after filtering in treatment: 26783993 INFO @ Sun, 21 Jun 2020 21:28:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:46: #2 number of paired peaks: 647 WARNING @ Sun, 21 Jun 2020 21:28:46: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sun, 21 Jun 2020 21:28:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:47: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:28:47: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 21:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.10_model.r WARNING @ Sun, 21 Jun 2020 21:28:47: #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 21:28:47: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 21:28:47: #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 21:28:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:51: 25000000 INFO @ Sun, 21 Jun 2020 21:28:58: 26000000 INFO @ Sun, 21 Jun 2020 21:28:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:04: #1 total tags in treatment: 26784050 INFO @ Sun, 21 Jun 2020 21:29:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:04: #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 21:29:05: #1 tags after filtering in treatment: 26783993 INFO @ Sun, 21 Jun 2020 21:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:07: #2 number of paired peaks: 647 WARNING @ Sun, 21 Jun 2020 21:29:07: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sun, 21 Jun 2020 21:29:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:07: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 21:29:07: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 21:29:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.20_model.r WARNING @ Sun, 21 Jun 2020 21:29:07: #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 21:29:07: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 21:29:07: #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 21:29:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.05_summits.bed INFO @ Sun, 21 Jun 2020 21:29:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.10_summits.bed INFO @ Sun, 21 Jun 2020 21:29:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664655/SRX4664655.20_summits.bed INFO @ Sun, 21 Jun 2020 21:30:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling