Job ID = 6457219 SRX = SRX457599 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:39:25 prefetch.2.10.7: 1) Downloading 'SRR1153275'... 2020-06-21T11:39:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:41:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:41:41 prefetch.2.10.7: 'SRR1153275' is valid 2020-06-21T11:41:41 prefetch.2.10.7: 1) 'SRR1153275' was downloaded successfully Read 7500488 spots for SRR1153275/SRR1153275.sra Written 7500488 spots for SRR1153275/SRR1153275.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: 00:02:03 7500488 reads; of these: 7500488 (100.00%) were unpaired; of these: 227926 (3.04%) aligned 0 times 5482609 (73.10%) aligned exactly 1 time 1789953 (23.86%) aligned >1 times 96.96% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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_rmdupse_core] 481510 / 7272562 = 0.0662 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 20:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.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 20:46:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:46:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:46:36: 1000000 INFO @ Sun, 21 Jun 2020 20:46:42: 2000000 INFO @ Sun, 21 Jun 2020 20:46:48: 3000000 INFO @ Sun, 21 Jun 2020 20:46:54: 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 20:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.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 20:47:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:47:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:47:00: 5000000 INFO @ Sun, 21 Jun 2020 20:47:06: 1000000 INFO @ Sun, 21 Jun 2020 20:47:07: 6000000 INFO @ Sun, 21 Jun 2020 20:47:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:47:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:47:12: #1 total tags in treatment: 6791052 INFO @ Sun, 21 Jun 2020 20:47:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:47:12: #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 20:47:12: 2000000 INFO @ Sun, 21 Jun 2020 20:47:12: #1 tags after filtering in treatment: 6791037 INFO @ Sun, 21 Jun 2020 20:47:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:47:12: #1 finished! INFO @ Sun, 21 Jun 2020 20:47:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:47:13: #2 number of paired peaks: 474 WARNING @ Sun, 21 Jun 2020 20:47:13: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sun, 21 Jun 2020 20:47:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:47:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:47:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:47:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:47:13: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:47:13: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 21 Jun 2020 20:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.05_model.r WARNING @ Sun, 21 Jun 2020 20:47:13: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:47:13: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 21 Jun 2020 20:47:13: #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 20:47:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:47:18: 3000000 INFO @ Sun, 21 Jun 2020 20:47:24: 4000000 INFO @ Sun, 21 Jun 2020 20:47:27: #3 Call peaks for each chromosome... 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 20:47:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.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 20:47:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:47:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:47:30: 5000000 INFO @ Sun, 21 Jun 2020 20:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.05_summits.bed INFO @ Sun, 21 Jun 2020 20:47:34: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (1698 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:47:36: 1000000 INFO @ Sun, 21 Jun 2020 20:47:36: 6000000 INFO @ Sun, 21 Jun 2020 20:47:42: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:47:42: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:47:42: #1 total tags in treatment: 6791052 INFO @ Sun, 21 Jun 2020 20:47:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:47:42: #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 20:47:42: 2000000 INFO @ Sun, 21 Jun 2020 20:47:42: #1 tags after filtering in treatment: 6791037 INFO @ Sun, 21 Jun 2020 20:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:47:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:47:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:47:42: #2 number of paired peaks: 474 WARNING @ Sun, 21 Jun 2020 20:47:42: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sun, 21 Jun 2020 20:47:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:47:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:47:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:47:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:47:42: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:47:42: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 21 Jun 2020 20:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.10_model.r WARNING @ Sun, 21 Jun 2020 20:47:42: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:47:42: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 21 Jun 2020 20:47:42: #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 20:47:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:47:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:47:48: 3000000 INFO @ Sun, 21 Jun 2020 20:47:53: 4000000 INFO @ Sun, 21 Jun 2020 20:47:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:47:59: 5000000 INFO @ Sun, 21 Jun 2020 20:48:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.10_summits.bed INFO @ Sun, 21 Jun 2020 20:48:04: Done! pass1 - making usageList (347 chroms): 1 millis pass2 - checking and writing primary data (810 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:48:05: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:48:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:48:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:48:10: #1 total tags in treatment: 6791052 INFO @ Sun, 21 Jun 2020 20:48:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:48:10: #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 20:48:11: #1 tags after filtering in treatment: 6791037 INFO @ Sun, 21 Jun 2020 20:48:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:48:11: #1 finished! INFO @ Sun, 21 Jun 2020 20:48:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:48:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:48:11: #2 number of paired peaks: 474 WARNING @ Sun, 21 Jun 2020 20:48:11: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sun, 21 Jun 2020 20:48:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:48:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:48:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:48:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:48:11: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:48:11: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 21 Jun 2020 20:48:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.20_model.r WARNING @ Sun, 21 Jun 2020 20:48:11: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:48:11: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 21 Jun 2020 20:48:11: #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 20:48:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:48:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:48:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX457599/SRX457599.20_summits.bed INFO @ Sun, 21 Jun 2020 20:48:33: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 4 millis CompletedMACS2peakCalling