Job ID = 6455009 SRX = SRX2618554 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:49:25 prefetch.2.10.7: 1) Downloading 'SRR5319108'... 2020-06-21T09:49:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:53:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:53:14 prefetch.2.10.7: 1) 'SRR5319108' was downloaded successfully 2020-06-21T09:53:14 prefetch.2.10.7: 'SRR5319108' has 0 unresolved dependencies Read 27915269 spots for SRR5319108/SRR5319108.sra Written 27915269 spots for SRR5319108/SRR5319108.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: 00:08:09 27915269 reads; of these: 27915269 (100.00%) were unpaired; of these: 1043794 (3.74%) aligned 0 times 19797586 (70.92%) aligned exactly 1 time 7073889 (25.34%) aligned >1 times 96.26% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 4079657 / 26871475 = 0.1518 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 19:10:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.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 19:10:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:43: 1000000 INFO @ Sun, 21 Jun 2020 19:10:50: 2000000 INFO @ Sun, 21 Jun 2020 19:10:56: 3000000 INFO @ Sun, 21 Jun 2020 19:11:03: 4000000 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 19:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.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 19:11:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:11: 5000000 INFO @ Sun, 21 Jun 2020 19:11:13: 1000000 INFO @ Sun, 21 Jun 2020 19:11:19: 2000000 INFO @ Sun, 21 Jun 2020 19:11:19: 6000000 INFO @ Sun, 21 Jun 2020 19:11:26: 3000000 INFO @ Sun, 21 Jun 2020 19:11:28: 7000000 INFO @ Sun, 21 Jun 2020 19:11:32: 4000000 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 19:11:36: 8000000 INFO @ Sun, 21 Jun 2020 19:11:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.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 19:11:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:39: 5000000 INFO @ Sun, 21 Jun 2020 19:11:44: 1000000 INFO @ Sun, 21 Jun 2020 19:11:44: 9000000 INFO @ Sun, 21 Jun 2020 19:11:46: 6000000 INFO @ Sun, 21 Jun 2020 19:11:50: 2000000 INFO @ Sun, 21 Jun 2020 19:11:53: 10000000 INFO @ Sun, 21 Jun 2020 19:11:53: 7000000 INFO @ Sun, 21 Jun 2020 19:11:57: 3000000 INFO @ Sun, 21 Jun 2020 19:12:01: 8000000 INFO @ Sun, 21 Jun 2020 19:12:01: 11000000 INFO @ Sun, 21 Jun 2020 19:12:04: 4000000 INFO @ Sun, 21 Jun 2020 19:12:08: 9000000 INFO @ Sun, 21 Jun 2020 19:12:09: 12000000 INFO @ Sun, 21 Jun 2020 19:12:11: 5000000 INFO @ Sun, 21 Jun 2020 19:12:16: 10000000 INFO @ Sun, 21 Jun 2020 19:12:17: 6000000 INFO @ Sun, 21 Jun 2020 19:12:18: 13000000 INFO @ Sun, 21 Jun 2020 19:12:23: 11000000 INFO @ Sun, 21 Jun 2020 19:12:24: 7000000 INFO @ Sun, 21 Jun 2020 19:12:26: 14000000 INFO @ Sun, 21 Jun 2020 19:12:31: 8000000 INFO @ Sun, 21 Jun 2020 19:12:31: 12000000 INFO @ Sun, 21 Jun 2020 19:12:35: 15000000 INFO @ Sun, 21 Jun 2020 19:12:37: 9000000 INFO @ Sun, 21 Jun 2020 19:12:38: 13000000 INFO @ Sun, 21 Jun 2020 19:12:43: 16000000 INFO @ Sun, 21 Jun 2020 19:12:44: 10000000 INFO @ Sun, 21 Jun 2020 19:12:46: 14000000 INFO @ Sun, 21 Jun 2020 19:12:50: 11000000 INFO @ Sun, 21 Jun 2020 19:12:52: 17000000 INFO @ Sun, 21 Jun 2020 19:12:53: 15000000 INFO @ Sun, 21 Jun 2020 19:12:57: 12000000 INFO @ Sun, 21 Jun 2020 19:13:01: 16000000 INFO @ Sun, 21 Jun 2020 19:13:01: 18000000 INFO @ Sun, 21 Jun 2020 19:13:04: 13000000 INFO @ Sun, 21 Jun 2020 19:13:10: 14000000 INFO @ Sun, 21 Jun 2020 19:13:10: 19000000 INFO @ Sun, 21 Jun 2020 19:13:11: 17000000 INFO @ Sun, 21 Jun 2020 19:13:17: 15000000 INFO @ Sun, 21 Jun 2020 19:13:19: 20000000 INFO @ Sun, 21 Jun 2020 19:13:19: 18000000 INFO @ Sun, 21 Jun 2020 19:13:23: 16000000 INFO @ Sun, 21 Jun 2020 19:13:27: 19000000 INFO @ Sun, 21 Jun 2020 19:13:27: 21000000 INFO @ Sun, 21 Jun 2020 19:13:30: 17000000 INFO @ Sun, 21 Jun 2020 19:13:34: 20000000 INFO @ Sun, 21 Jun 2020 19:13:35: 22000000 INFO @ Sun, 21 Jun 2020 19:13:38: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:13:41: 21000000 INFO @ Sun, 21 Jun 2020 19:13:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:43: #1 total tags in treatment: 22791818 INFO @ Sun, 21 Jun 2020 19:13:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:43: #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 19:13:43: #1 tags after filtering in treatment: 22791817 INFO @ Sun, 21 Jun 2020 19:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:45: 19000000 INFO @ Sun, 21 Jun 2020 19:13:45: #2 number of paired peaks: 472 WARNING @ Sun, 21 Jun 2020 19:13:45: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:45: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:13:45: #2 alternative fragment length(s) may be 2,31,587,597 bps INFO @ Sun, 21 Jun 2020 19:13:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.05_model.r WARNING @ Sun, 21 Jun 2020 19:13:45: #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 19:13:45: #2 You may need to consider one of the other alternative d(s): 2,31,587,597 WARNING @ Sun, 21 Jun 2020 19:13:45: #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 19:13:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:48: 22000000 INFO @ Sun, 21 Jun 2020 19:13:52: 20000000 INFO @ Sun, 21 Jun 2020 19:13:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:55: #1 total tags in treatment: 22791818 INFO @ Sun, 21 Jun 2020 19:13:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:55: #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 19:13:56: #1 tags after filtering in treatment: 22791817 INFO @ Sun, 21 Jun 2020 19:13:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:58: #2 number of paired peaks: 472 WARNING @ Sun, 21 Jun 2020 19:13:58: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:58: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:58: 21000000 INFO @ Sun, 21 Jun 2020 19:13:58: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:58: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:13:58: #2 alternative fragment length(s) may be 2,31,587,597 bps INFO @ Sun, 21 Jun 2020 19:13:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.10_model.r WARNING @ Sun, 21 Jun 2020 19:13:58: #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 19:13:58: #2 You may need to consider one of the other alternative d(s): 2,31,587,597 WARNING @ Sun, 21 Jun 2020 19:13:58: #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 19:13:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:04: 22000000 INFO @ Sun, 21 Jun 2020 19:14:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:09: #1 total tags in treatment: 22791818 INFO @ Sun, 21 Jun 2020 19:14:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:09: #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 19:14:10: #1 tags after filtering in treatment: 22791817 INFO @ Sun, 21 Jun 2020 19:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:12: #2 number of paired peaks: 472 WARNING @ Sun, 21 Jun 2020 19:14:12: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:12: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:14:12: #2 alternative fragment length(s) may be 2,31,587,597 bps INFO @ Sun, 21 Jun 2020 19:14:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.20_model.r WARNING @ Sun, 21 Jun 2020 19:14:12: #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 19:14:12: #2 You may need to consider one of the other alternative d(s): 2,31,587,597 WARNING @ Sun, 21 Jun 2020 19:14:12: #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 19:14:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.05_summits.bed INFO @ Sun, 21 Jun 2020 19:14:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.10_summits.bed INFO @ Sun, 21 Jun 2020 19:14:51: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618554/SRX2618554.20_summits.bed INFO @ Sun, 21 Jun 2020 19:15:05: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling