Job ID = 6453222 SRX = SRX1091593 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:04:38 prefetch.2.10.7: 1) Downloading 'SRR2096477'... 2020-06-21T08:04:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:08:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:08:33 prefetch.2.10.7: 1) 'SRR2096477' was downloaded successfully 2020-06-21T08:08:33 prefetch.2.10.7: 'SRR2096477' has 0 unresolved dependencies Read 10479960 spots for SRR2096477/SRR2096477.sra Written 10479960 spots for SRR2096477/SRR2096477.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: 00:07:31 10479960 reads; of these: 10479960 (100.00%) were unpaired; of these: 264718 (2.53%) aligned 0 times 8267024 (78.88%) aligned exactly 1 time 1948218 (18.59%) aligned >1 times 97.47% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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 8 files... [bam_rmdupse_core] 673621 / 10215242 = 0.0659 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 17:22:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.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 17:22:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:27: 1000000 INFO @ Sun, 21 Jun 2020 17:22:37: 2000000 INFO @ Sun, 21 Jun 2020 17:22:46: 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 17:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.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 17:22:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:56: 4000000 INFO @ Sun, 21 Jun 2020 17:22:59: 1000000 INFO @ Sun, 21 Jun 2020 17:23:06: 5000000 INFO @ Sun, 21 Jun 2020 17:23:09: 2000000 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 17:23:17: 6000000 INFO @ Sun, 21 Jun 2020 17:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.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 17:23:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:20: 3000000 INFO @ Sun, 21 Jun 2020 17:23:27: 7000000 INFO @ Sun, 21 Jun 2020 17:23:29: 1000000 INFO @ Sun, 21 Jun 2020 17:23:30: 4000000 INFO @ Sun, 21 Jun 2020 17:23:38: 8000000 INFO @ Sun, 21 Jun 2020 17:23:40: 2000000 INFO @ Sun, 21 Jun 2020 17:23:41: 5000000 INFO @ Sun, 21 Jun 2020 17:23:49: 9000000 INFO @ Sun, 21 Jun 2020 17:23:51: 3000000 INFO @ Sun, 21 Jun 2020 17:23:52: 6000000 INFO @ Sun, 21 Jun 2020 17:23:55: #1 tag size is determined as 148 bps INFO @ Sun, 21 Jun 2020 17:23:55: #1 tag size = 148 INFO @ Sun, 21 Jun 2020 17:23:55: #1 total tags in treatment: 9541621 INFO @ Sun, 21 Jun 2020 17:23:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:55: #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 17:23:55: #1 tags after filtering in treatment: 9541573 INFO @ Sun, 21 Jun 2020 17:23:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:56: #2 number of paired peaks: 461 WARNING @ Sun, 21 Jun 2020 17:23:56: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sun, 21 Jun 2020 17:23:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:56: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 17:23:56: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 17:23:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.05_model.r WARNING @ Sun, 21 Jun 2020 17:23:56: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:23:56: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 21 Jun 2020 17:23:56: #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 17:23:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:24:01: 4000000 INFO @ Sun, 21 Jun 2020 17:24:02: 7000000 INFO @ Sun, 21 Jun 2020 17:24:12: 5000000 INFO @ Sun, 21 Jun 2020 17:24:14: 8000000 INFO @ Sun, 21 Jun 2020 17:24:17: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:24:23: 6000000 INFO @ Sun, 21 Jun 2020 17:24:24: 9000000 INFO @ Sun, 21 Jun 2020 17:24:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.05_summits.bed INFO @ Sun, 21 Jun 2020 17:24:27: Done! pass1 - making usageList (576 chroms): 2 millis pass2 - checking and writing primary data (2850 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:24:30: #1 tag size is determined as 148 bps INFO @ Sun, 21 Jun 2020 17:24:30: #1 tag size = 148 INFO @ Sun, 21 Jun 2020 17:24:30: #1 total tags in treatment: 9541621 INFO @ Sun, 21 Jun 2020 17:24:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:30: #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 17:24:30: #1 tags after filtering in treatment: 9541573 INFO @ Sun, 21 Jun 2020 17:24:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:30: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:31: #2 number of paired peaks: 461 WARNING @ Sun, 21 Jun 2020 17:24:31: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sun, 21 Jun 2020 17:24:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:31: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 17:24:31: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 17:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.10_model.r WARNING @ Sun, 21 Jun 2020 17:24:31: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:24:31: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 21 Jun 2020 17:24:31: #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 17:24:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:24:33: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:24:43: 8000000 INFO @ Sun, 21 Jun 2020 17:24:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:52: 9000000 INFO @ Sun, 21 Jun 2020 17:24:57: #1 tag size is determined as 148 bps INFO @ Sun, 21 Jun 2020 17:24:57: #1 tag size = 148 INFO @ Sun, 21 Jun 2020 17:24:57: #1 total tags in treatment: 9541621 INFO @ Sun, 21 Jun 2020 17:24:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:57: #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 17:24:58: #1 tags after filtering in treatment: 9541573 INFO @ Sun, 21 Jun 2020 17:24:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:58: #2 number of paired peaks: 461 WARNING @ Sun, 21 Jun 2020 17:24:58: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sun, 21 Jun 2020 17:24:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:58: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:58: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:58: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 17:24:58: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 17:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.20_model.r WARNING @ Sun, 21 Jun 2020 17:24:59: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:24:59: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 21 Jun 2020 17:24:59: #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 17:24:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:25:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:25:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:25:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.10_summits.bed INFO @ Sun, 21 Jun 2020 17:25:02: Done! pass1 - making usageList (445 chroms): 1 millis pass2 - checking and writing primary data (1085 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:25:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:25:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:25:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091593/SRX1091593.20_summits.bed INFO @ Sun, 21 Jun 2020 17:25:29: Done! pass1 - making usageList (297 chroms): 1 millis pass2 - checking and writing primary data (507 records, 4 fields): 9 millis CompletedMACS2peakCalling