Job ID = 6527636 SRX = SRX182774 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:47:37 prefetch.2.10.7: 1) Downloading 'SRR553568'... 2020-06-29T12:47:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:50:08 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:50:08 prefetch.2.10.7: 1) 'SRR553568' was downloaded successfully Read 27246731 spots for SRR553568/SRR553568.sra Written 27246731 spots for SRR553568/SRR553568.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: 00:09:15 27246731 reads; of these: 27246731 (100.00%) were unpaired; of these: 1262746 (4.63%) aligned 0 times 17705624 (64.98%) aligned exactly 1 time 8278361 (30.38%) aligned >1 times 95.37% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 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 8 files... [bam_rmdupse_core] 3997403 / 25983985 = 0.1538 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 22:11:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.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 22:11:08: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:11:08: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:11:13: 1000000 INFO @ Mon, 29 Jun 2020 22:11:17: 2000000 INFO @ Mon, 29 Jun 2020 22:11:22: 3000000 INFO @ Mon, 29 Jun 2020 22:11:26: 4000000 INFO @ Mon, 29 Jun 2020 22:11:30: 5000000 INFO @ Mon, 29 Jun 2020 22:11:35: 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 @ Mon, 29 Jun 2020 22:11:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.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 22:11:38: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:11:38: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:11:39: 7000000 INFO @ Mon, 29 Jun 2020 22:11:43: 1000000 INFO @ Mon, 29 Jun 2020 22:11:44: 8000000 INFO @ Mon, 29 Jun 2020 22:11:47: 2000000 INFO @ Mon, 29 Jun 2020 22:11:48: 9000000 INFO @ Mon, 29 Jun 2020 22:11:51: 3000000 INFO @ Mon, 29 Jun 2020 22:11:53: 10000000 INFO @ Mon, 29 Jun 2020 22:11:56: 4000000 INFO @ Mon, 29 Jun 2020 22:11:57: 11000000 INFO @ Mon, 29 Jun 2020 22:12:00: 5000000 INFO @ Mon, 29 Jun 2020 22:12:02: 12000000 INFO @ Mon, 29 Jun 2020 22:12:05: 6000000 INFO @ Mon, 29 Jun 2020 22:12:06: 13000000 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 22:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.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 22:12:08: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:12:08: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:12:09: 7000000 INFO @ Mon, 29 Jun 2020 22:12:11: 14000000 INFO @ Mon, 29 Jun 2020 22:12:13: 1000000 INFO @ Mon, 29 Jun 2020 22:12:14: 8000000 INFO @ Mon, 29 Jun 2020 22:12:15: 15000000 INFO @ Mon, 29 Jun 2020 22:12:17: 2000000 INFO @ Mon, 29 Jun 2020 22:12:18: 9000000 INFO @ Mon, 29 Jun 2020 22:12:20: 16000000 INFO @ Mon, 29 Jun 2020 22:12:22: 3000000 INFO @ Mon, 29 Jun 2020 22:12:22: 10000000 INFO @ Mon, 29 Jun 2020 22:12:24: 17000000 INFO @ Mon, 29 Jun 2020 22:12:26: 4000000 INFO @ Mon, 29 Jun 2020 22:12:27: 11000000 INFO @ Mon, 29 Jun 2020 22:12:29: 18000000 INFO @ Mon, 29 Jun 2020 22:12:30: 5000000 INFO @ Mon, 29 Jun 2020 22:12:31: 12000000 INFO @ Mon, 29 Jun 2020 22:12:33: 19000000 INFO @ Mon, 29 Jun 2020 22:12:35: 6000000 INFO @ Mon, 29 Jun 2020 22:12:36: 13000000 INFO @ Mon, 29 Jun 2020 22:12:37: 20000000 INFO @ Mon, 29 Jun 2020 22:12:39: 7000000 INFO @ Mon, 29 Jun 2020 22:12:40: 14000000 INFO @ Mon, 29 Jun 2020 22:12:42: 21000000 INFO @ Mon, 29 Jun 2020 22:12:44: 8000000 INFO @ Mon, 29 Jun 2020 22:12:44: 15000000 INFO @ Mon, 29 Jun 2020 22:12:46: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:12:46: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:12:46: #1 total tags in treatment: 21986582 INFO @ Mon, 29 Jun 2020 22:12:46: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:12:46: #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 22:12:47: #1 tags after filtering in treatment: 21986582 INFO @ Mon, 29 Jun 2020 22:12:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:12:47: #1 finished! INFO @ Mon, 29 Jun 2020 22:12:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:12:48: #2 number of paired peaks: 133 WARNING @ Mon, 29 Jun 2020 22:12:48: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Mon, 29 Jun 2020 22:12:48: start model_add_line... INFO @ Mon, 29 Jun 2020 22:12:48: start X-correlation... INFO @ Mon, 29 Jun 2020 22:12:48: end of X-cor INFO @ Mon, 29 Jun 2020 22:12:48: #2 finished! INFO @ Mon, 29 Jun 2020 22:12:48: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 22:12:48: #2 alternative fragment length(s) may be 33 bps INFO @ Mon, 29 Jun 2020 22:12:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.05_model.r INFO @ Mon, 29 Jun 2020 22:12:48: 9000000 WARNING @ Mon, 29 Jun 2020 22:12:48: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:12:48: #2 You may need to consider one of the other alternative d(s): 33 WARNING @ Mon, 29 Jun 2020 22:12:48: #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 22:12:48: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:12:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:12:49: 16000000 INFO @ Mon, 29 Jun 2020 22:12:53: 10000000 INFO @ Mon, 29 Jun 2020 22:12:53: 17000000 INFO @ Mon, 29 Jun 2020 22:12:57: 11000000 INFO @ Mon, 29 Jun 2020 22:12:57: 18000000 INFO @ Mon, 29 Jun 2020 22:13:02: 12000000 INFO @ Mon, 29 Jun 2020 22:13:02: 19000000 INFO @ Mon, 29 Jun 2020 22:13:06: 13000000 INFO @ Mon, 29 Jun 2020 22:13:06: 20000000 INFO @ Mon, 29 Jun 2020 22:13:10: 14000000 INFO @ Mon, 29 Jun 2020 22:13:10: 21000000 INFO @ Mon, 29 Jun 2020 22:13:15: 15000000 INFO @ Mon, 29 Jun 2020 22:13:15: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:13:15: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:13:15: #1 total tags in treatment: 21986582 INFO @ Mon, 29 Jun 2020 22:13:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:13:15: #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 22:13:15: #1 tags after filtering in treatment: 21986582 INFO @ Mon, 29 Jun 2020 22:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:13:15: #1 finished! INFO @ Mon, 29 Jun 2020 22:13:15: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:13:17: #2 number of paired peaks: 133 WARNING @ Mon, 29 Jun 2020 22:13:17: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Mon, 29 Jun 2020 22:13:17: start model_add_line... INFO @ Mon, 29 Jun 2020 22:13:17: start X-correlation... INFO @ Mon, 29 Jun 2020 22:13:17: end of X-cor INFO @ Mon, 29 Jun 2020 22:13:17: #2 finished! INFO @ Mon, 29 Jun 2020 22:13:17: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 22:13:17: #2 alternative fragment length(s) may be 33 bps INFO @ Mon, 29 Jun 2020 22:13:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.10_model.r WARNING @ Mon, 29 Jun 2020 22:13:17: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:13:17: #2 You may need to consider one of the other alternative d(s): 33 WARNING @ Mon, 29 Jun 2020 22:13:17: #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 22:13:17: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:13:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:13:19: 16000000 INFO @ Mon, 29 Jun 2020 22:13:24: 17000000 INFO @ Mon, 29 Jun 2020 22:13:27: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:13:28: 18000000 INFO @ Mon, 29 Jun 2020 22:13:32: 19000000 INFO @ Mon, 29 Jun 2020 22:13:37: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:13:41: 21000000 INFO @ Mon, 29 Jun 2020 22:13:46: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:13:46: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:13:46: #1 total tags in treatment: 21986582 INFO @ Mon, 29 Jun 2020 22:13:46: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:13:46: #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 22:13:46: #1 tags after filtering in treatment: 21986582 INFO @ Mon, 29 Jun 2020 22:13:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:13:46: #1 finished! INFO @ Mon, 29 Jun 2020 22:13:46: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:13:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.05_summits.bed INFO @ Mon, 29 Jun 2020 22:13:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2521 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:13:47: #2 number of paired peaks: 133 WARNING @ Mon, 29 Jun 2020 22:13:47: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Mon, 29 Jun 2020 22:13:47: start model_add_line... INFO @ Mon, 29 Jun 2020 22:13:47: start X-correlation... INFO @ Mon, 29 Jun 2020 22:13:47: end of X-cor INFO @ Mon, 29 Jun 2020 22:13:47: #2 finished! INFO @ Mon, 29 Jun 2020 22:13:47: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 22:13:47: #2 alternative fragment length(s) may be 33 bps INFO @ Mon, 29 Jun 2020 22:13:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.20_model.r WARNING @ Mon, 29 Jun 2020 22:13:47: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:13:47: #2 You may need to consider one of the other alternative d(s): 33 WARNING @ Mon, 29 Jun 2020 22:13:47: #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 22:13:47: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:13:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:13:55: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:14:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:14:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.10_summits.bed INFO @ Mon, 29 Jun 2020 22:14:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1876 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:14:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:14:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:14:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:14:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX182774/SRX182774.20_summits.bed INFO @ Mon, 29 Jun 2020 22:14:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1189 records, 4 fields): 3 millis CompletedMACS2peakCalling