Job ID = 6458354 SRX = SRX5011095 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:07 prefetch.2.10.7: 1) Downloading 'SRR8191544'... 2020-06-21T12:31:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:33:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:33:37 prefetch.2.10.7: 'SRR8191544' is valid 2020-06-21T12:33:37 prefetch.2.10.7: 1) 'SRR8191544' was downloaded successfully 2020-06-21T12:33:37 prefetch.2.10.7: 'SRR8191544' has 0 unresolved dependencies Read 29208741 spots for SRR8191544/SRR8191544.sra Written 29208741 spots for SRR8191544/SRR8191544.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: 00:07:26 29208741 reads; of these: 29208741 (100.00%) were unpaired; of these: 3838475 (13.14%) aligned 0 times 18354349 (62.84%) aligned exactly 1 time 7015917 (24.02%) aligned >1 times 86.86% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 13189855 / 25370266 = 0.5199 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 21:46:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.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 21:46:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:38: 1000000 INFO @ Sun, 21 Jun 2020 21:46:42: 2000000 INFO @ Sun, 21 Jun 2020 21:46:47: 3000000 INFO @ Sun, 21 Jun 2020 21:46:52: 4000000 INFO @ Sun, 21 Jun 2020 21:46:56: 5000000 INFO @ Sun, 21 Jun 2020 21:47:01: 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 @ Sun, 21 Jun 2020 21:47:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.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 21:47:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:47:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:47:05: 7000000 INFO @ Sun, 21 Jun 2020 21:47:07: 1000000 INFO @ Sun, 21 Jun 2020 21:47:10: 8000000 INFO @ Sun, 21 Jun 2020 21:47:12: 2000000 INFO @ Sun, 21 Jun 2020 21:47:15: 9000000 INFO @ Sun, 21 Jun 2020 21:47:17: 3000000 INFO @ Sun, 21 Jun 2020 21:47:20: 10000000 INFO @ Sun, 21 Jun 2020 21:47:21: 4000000 INFO @ Sun, 21 Jun 2020 21:47:24: 11000000 INFO @ Sun, 21 Jun 2020 21:47:26: 5000000 INFO @ Sun, 21 Jun 2020 21:47:29: 12000000 INFO @ Sun, 21 Jun 2020 21:47:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:30: #1 total tags in treatment: 12180411 INFO @ Sun, 21 Jun 2020 21:47:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:30: #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 21:47:30: #1 tags after filtering in treatment: 12180347 INFO @ Sun, 21 Jun 2020 21:47:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:31: 6000000 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 21:47:31: #2 number of paired peaks: 2118 INFO @ Sun, 21 Jun 2020 21:47:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:31: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 21:47:31: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 21:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.05_model.r WARNING @ Sun, 21 Jun 2020 21:47:31: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:47:31: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 21:47:31: #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 21:47:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.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 21:47:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:47:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:47:36: 7000000 INFO @ Sun, 21 Jun 2020 21:47:38: 1000000 INFO @ Sun, 21 Jun 2020 21:47:41: 8000000 INFO @ Sun, 21 Jun 2020 21:47:43: 2000000 INFO @ Sun, 21 Jun 2020 21:47:45: 9000000 INFO @ Sun, 21 Jun 2020 21:47:47: 3000000 INFO @ Sun, 21 Jun 2020 21:47:51: 10000000 INFO @ Sun, 21 Jun 2020 21:47:52: 4000000 INFO @ Sun, 21 Jun 2020 21:47:55: 11000000 INFO @ Sun, 21 Jun 2020 21:47:57: 5000000 INFO @ Sun, 21 Jun 2020 21:47:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:00: 12000000 INFO @ Sun, 21 Jun 2020 21:48:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:48:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:48:01: #1 total tags in treatment: 12180411 INFO @ Sun, 21 Jun 2020 21:48:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:01: #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 21:48:02: #1 tags after filtering in treatment: 12180347 INFO @ Sun, 21 Jun 2020 21:48:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:02: 6000000 INFO @ Sun, 21 Jun 2020 21:48:03: #2 number of paired peaks: 2118 INFO @ Sun, 21 Jun 2020 21:48:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:03: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 21:48:03: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 21:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.10_model.r WARNING @ Sun, 21 Jun 2020 21:48:03: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:48:03: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 21:48:03: #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 21:48:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:07: 7000000 INFO @ Sun, 21 Jun 2020 21:48:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.05_summits.bed INFO @ Sun, 21 Jun 2020 21:48:10: Done! pass1 - making usageList (779 chroms): 2 millis pass2 - checking and writing primary data (3986 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:12: 8000000 INFO @ Sun, 21 Jun 2020 21:48:16: 9000000 INFO @ Sun, 21 Jun 2020 21:48:21: 10000000 INFO @ Sun, 21 Jun 2020 21:48:26: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:48:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:31: 12000000 INFO @ Sun, 21 Jun 2020 21:48:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:48:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:48:32: #1 total tags in treatment: 12180411 INFO @ Sun, 21 Jun 2020 21:48:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:32: #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 21:48:33: #1 tags after filtering in treatment: 12180347 INFO @ Sun, 21 Jun 2020 21:48:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:34: #2 number of paired peaks: 2118 INFO @ Sun, 21 Jun 2020 21:48:34: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:34: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:34: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:34: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:34: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 21:48:34: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 21:48:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.20_model.r WARNING @ Sun, 21 Jun 2020 21:48:34: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:48:34: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 21:48:34: #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 21:48:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.10_summits.bed INFO @ Sun, 21 Jun 2020 21:48:40: Done! pass1 - making usageList (672 chroms): 2 millis pass2 - checking and writing primary data (2639 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:49:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:49:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:49:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:49:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011095/SRX5011095.20_summits.bed INFO @ Sun, 21 Jun 2020 21:49:12: Done! pass1 - making usageList (419 chroms): 1 millis pass2 - checking and writing primary data (1015 records, 4 fields): 13 millis CompletedMACS2peakCalling