Job ID = 6527839 SRX = SRX287834 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:44:59 prefetch.2.10.7: 1) Downloading 'SRR870023'... 2020-06-29T13:44:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:54:57 prefetch.2.10.7: HTTPS download failed 2020-06-29T13:54:57 prefetch.2.10.7: 1) failed to download SRR870023 2020-06-29T13:55:07 prefetch.2.10.7: 1) Downloading 'SRR870023'... 2020-06-29T13:55:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:55:07 prefetch.2.10.7: Continue download of 'SRR870023' from 775170242 2020-06-29T13:55:15 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:55:15 prefetch.2.10.7: 1) 'SRR870023' was downloaded successfully Read 22109731 spots for SRR870023/SRR870023.sra Written 22109731 spots for SRR870023/SRR870023.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:48 22109731 reads; of these: 22109731 (100.00%) were unpaired; of these: 1293818 (5.85%) aligned 0 times 13813367 (62.48%) aligned exactly 1 time 7002546 (31.67%) aligned >1 times 94.15% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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 12 files... [bam_rmdupse_core] 3521430 / 20815913 = 0.1692 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 @ Mon, 29 Jun 2020 23:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.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 @ Mon, 29 Jun 2020 23:14:17: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:14:17: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:14:24: 1000000 INFO @ Mon, 29 Jun 2020 23:14:31: 2000000 INFO @ Mon, 29 Jun 2020 23:14:37: 3000000 INFO @ Mon, 29 Jun 2020 23:14:43: 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 @ Mon, 29 Jun 2020 23:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.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 @ Mon, 29 Jun 2020 23:14:47: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:14:47: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:14:49: 5000000 INFO @ Mon, 29 Jun 2020 23:14:55: 1000000 INFO @ Mon, 29 Jun 2020 23:14:56: 6000000 INFO @ Mon, 29 Jun 2020 23:15:01: 2000000 INFO @ Mon, 29 Jun 2020 23:15:02: 7000000 INFO @ Mon, 29 Jun 2020 23:15:07: 3000000 INFO @ Mon, 29 Jun 2020 23:15:09: 8000000 INFO @ Mon, 29 Jun 2020 23:15:14: 4000000 INFO @ Mon, 29 Jun 2020 23:15:15: 9000000 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 @ Mon, 29 Jun 2020 23:15:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.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 @ Mon, 29 Jun 2020 23:15:17: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:15:17: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:15:21: 5000000 INFO @ Mon, 29 Jun 2020 23:15:22: 10000000 INFO @ Mon, 29 Jun 2020 23:15:24: 1000000 INFO @ Mon, 29 Jun 2020 23:15:27: 6000000 INFO @ Mon, 29 Jun 2020 23:15:28: 11000000 INFO @ Mon, 29 Jun 2020 23:15:32: 2000000 INFO @ Mon, 29 Jun 2020 23:15:34: 7000000 INFO @ Mon, 29 Jun 2020 23:15:35: 12000000 INFO @ Mon, 29 Jun 2020 23:15:39: 3000000 INFO @ Mon, 29 Jun 2020 23:15:41: 8000000 INFO @ Mon, 29 Jun 2020 23:15:42: 13000000 INFO @ Mon, 29 Jun 2020 23:15:45: 4000000 INFO @ Mon, 29 Jun 2020 23:15:48: 9000000 INFO @ Mon, 29 Jun 2020 23:15:49: 14000000 INFO @ Mon, 29 Jun 2020 23:15:52: 5000000 INFO @ Mon, 29 Jun 2020 23:15:55: 10000000 INFO @ Mon, 29 Jun 2020 23:15:56: 15000000 INFO @ Mon, 29 Jun 2020 23:15:59: 6000000 INFO @ Mon, 29 Jun 2020 23:16:01: 11000000 INFO @ Mon, 29 Jun 2020 23:16:03: 16000000 INFO @ Mon, 29 Jun 2020 23:16:06: 7000000 INFO @ Mon, 29 Jun 2020 23:16:08: 12000000 INFO @ Mon, 29 Jun 2020 23:16:10: 17000000 INFO @ Mon, 29 Jun 2020 23:16:12: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:16:12: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:16:12: #1 total tags in treatment: 17294483 INFO @ Mon, 29 Jun 2020 23:16:12: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:16:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:16:12: #1 tags after filtering in treatment: 17294483 INFO @ Mon, 29 Jun 2020 23:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:16:12: #1 finished! INFO @ Mon, 29 Jun 2020 23:16:12: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:16:13: 8000000 INFO @ Mon, 29 Jun 2020 23:16:14: #2 number of paired peaks: 191 WARNING @ Mon, 29 Jun 2020 23:16:14: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 29 Jun 2020 23:16:14: start model_add_line... INFO @ Mon, 29 Jun 2020 23:16:14: start X-correlation... INFO @ Mon, 29 Jun 2020 23:16:14: end of X-cor INFO @ Mon, 29 Jun 2020 23:16:14: #2 finished! INFO @ Mon, 29 Jun 2020 23:16:14: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 23:16:14: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 23:16:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.05_model.r WARNING @ Mon, 29 Jun 2020 23:16:14: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:16:14: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 23:16:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:16:14: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:16:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:16:15: 13000000 INFO @ Mon, 29 Jun 2020 23:16:19: 9000000 INFO @ Mon, 29 Jun 2020 23:16:22: 14000000 INFO @ Mon, 29 Jun 2020 23:16:26: 10000000 INFO @ Mon, 29 Jun 2020 23:16:29: 15000000 INFO @ Mon, 29 Jun 2020 23:16:32: 11000000 INFO @ Mon, 29 Jun 2020 23:16:36: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:16:40: 12000000 INFO @ Mon, 29 Jun 2020 23:16:43: 17000000 INFO @ Mon, 29 Jun 2020 23:16:44: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:16:46: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:16:46: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:16:46: #1 total tags in treatment: 17294483 INFO @ Mon, 29 Jun 2020 23:16:46: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:16:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:16:46: #1 tags after filtering in treatment: 17294483 INFO @ Mon, 29 Jun 2020 23:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:16:46: #1 finished! INFO @ Mon, 29 Jun 2020 23:16:46: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:16:47: 13000000 INFO @ Mon, 29 Jun 2020 23:16:47: #2 number of paired peaks: 191 WARNING @ Mon, 29 Jun 2020 23:16:47: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 29 Jun 2020 23:16:47: start model_add_line... INFO @ Mon, 29 Jun 2020 23:16:47: start X-correlation... INFO @ Mon, 29 Jun 2020 23:16:47: end of X-cor INFO @ Mon, 29 Jun 2020 23:16:47: #2 finished! INFO @ Mon, 29 Jun 2020 23:16:47: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 23:16:47: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 23:16:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.10_model.r WARNING @ Mon, 29 Jun 2020 23:16:47: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:16:47: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 23:16:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:16:47: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:16:53: 14000000 INFO @ Mon, 29 Jun 2020 23:17:00: 15000000 INFO @ Mon, 29 Jun 2020 23:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.05_summits.bed INFO @ Mon, 29 Jun 2020 23:17:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2183 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:17:07: 16000000 INFO @ Mon, 29 Jun 2020 23:17:13: 17000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:17:15: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:17:15: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:17:15: #1 total tags in treatment: 17294483 INFO @ Mon, 29 Jun 2020 23:17:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:17:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:17:15: #1 tags after filtering in treatment: 17294483 INFO @ Mon, 29 Jun 2020 23:17:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:17:15: #1 finished! INFO @ Mon, 29 Jun 2020 23:17:15: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:17:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:17:16: #2 number of paired peaks: 191 WARNING @ Mon, 29 Jun 2020 23:17:16: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 29 Jun 2020 23:17:16: start model_add_line... INFO @ Mon, 29 Jun 2020 23:17:17: start X-correlation... INFO @ Mon, 29 Jun 2020 23:17:17: end of X-cor INFO @ Mon, 29 Jun 2020 23:17:17: #2 finished! INFO @ Mon, 29 Jun 2020 23:17:17: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 23:17:17: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 23:17:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.20_model.r WARNING @ Mon, 29 Jun 2020 23:17:17: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:17:17: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 23:17:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:17:17: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:17:18: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:17:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:17:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:17:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.10_summits.bed INFO @ Mon, 29 Jun 2020 23:17:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1834 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:17:49: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287834/SRX287834.20_summits.bed INFO @ Mon, 29 Jun 2020 23:18:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1362 records, 4 fields): 3 millis CompletedMACS2peakCalling