Job ID = 6453464 SRX = SRX1158170 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:27:26 prefetch.2.10.7: 1) Downloading 'SRR2173469'... 2020-06-21T08:27:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:40:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:40:16 prefetch.2.10.7: 1) 'SRR2173469' was downloaded successfully Read 23457086 spots for SRR2173469/SRR2173469.sra Written 23457086 spots for SRR2173469/SRR2173469.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: 00:15:07 23457086 reads; of these: 23457086 (100.00%) were unpaired; of these: 1549741 (6.61%) aligned 0 times 13366883 (56.98%) aligned exactly 1 time 8540462 (36.41%) aligned >1 times 93.39% overall alignment rate Time searching: 00:15:07 Overall time: 00:15:07 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] 11880884 / 21907345 = 0.5423 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 18:04:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.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 18:04:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:04:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:04:37: 1000000 INFO @ Sun, 21 Jun 2020 18:04:44: 2000000 INFO @ Sun, 21 Jun 2020 18:04:52: 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 18:04:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.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 18:04:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:04:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:00: 4000000 INFO @ Sun, 21 Jun 2020 18:05:06: 1000000 INFO @ Sun, 21 Jun 2020 18:05:09: 5000000 INFO @ Sun, 21 Jun 2020 18:05:13: 2000000 INFO @ Sun, 21 Jun 2020 18:05:17: 6000000 INFO @ Sun, 21 Jun 2020 18:05:21: 3000000 INFO @ Sun, 21 Jun 2020 18:05:25: 7000000 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 18:05:28: 4000000 INFO @ Sun, 21 Jun 2020 18:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.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 18:05:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:33: 8000000 INFO @ Sun, 21 Jun 2020 18:05:36: 5000000 INFO @ Sun, 21 Jun 2020 18:05:36: 1000000 INFO @ Sun, 21 Jun 2020 18:05:41: 9000000 INFO @ Sun, 21 Jun 2020 18:05:43: 6000000 INFO @ Sun, 21 Jun 2020 18:05:44: 2000000 INFO @ Sun, 21 Jun 2020 18:05:50: 10000000 INFO @ Sun, 21 Jun 2020 18:05:50: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:05:50: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:05:50: #1 total tags in treatment: 10026461 INFO @ Sun, 21 Jun 2020 18:05:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:05:50: #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 18:05:50: #1 tags after filtering in treatment: 10026345 INFO @ Sun, 21 Jun 2020 18:05:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:05:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:05:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:05:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:05:51: 7000000 INFO @ Sun, 21 Jun 2020 18:05:51: 3000000 INFO @ Sun, 21 Jun 2020 18:05:51: #2 number of paired peaks: 2557 INFO @ Sun, 21 Jun 2020 18:05:51: start model_add_line... INFO @ Sun, 21 Jun 2020 18:05:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:05:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:05:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:05:51: #2 predicted fragment length is 108 bps INFO @ Sun, 21 Jun 2020 18:05:51: #2 alternative fragment length(s) may be 3,108 bps INFO @ Sun, 21 Jun 2020 18:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.05_model.r WARNING @ Sun, 21 Jun 2020 18:05:51: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:05:51: #2 You may need to consider one of the other alternative d(s): 3,108 WARNING @ Sun, 21 Jun 2020 18:05:51: #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 18:05:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:05:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:05:58: 8000000 INFO @ Sun, 21 Jun 2020 18:05:58: 4000000 INFO @ Sun, 21 Jun 2020 18:06:05: 5000000 INFO @ Sun, 21 Jun 2020 18:06:06: 9000000 INFO @ Sun, 21 Jun 2020 18:06:12: 6000000 INFO @ Sun, 21 Jun 2020 18:06:13: 10000000 INFO @ Sun, 21 Jun 2020 18:06:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:06:13: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:06:13: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:06:13: #1 total tags in treatment: 10026461 INFO @ Sun, 21 Jun 2020 18:06:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:13: #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 18:06:14: #1 tags after filtering in treatment: 10026345 INFO @ Sun, 21 Jun 2020 18:06:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:14: #2 number of paired peaks: 2557 INFO @ Sun, 21 Jun 2020 18:06:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:14: #2 predicted fragment length is 108 bps INFO @ Sun, 21 Jun 2020 18:06:14: #2 alternative fragment length(s) may be 3,108 bps INFO @ Sun, 21 Jun 2020 18:06:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.10_model.r WARNING @ Sun, 21 Jun 2020 18:06:14: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:06:14: #2 You may need to consider one of the other alternative d(s): 3,108 WARNING @ Sun, 21 Jun 2020 18:06:14: #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 18:06:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:06:19: 7000000 INFO @ Sun, 21 Jun 2020 18:06:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:06:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:06:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.05_summits.bed INFO @ Sun, 21 Jun 2020 18:06:24: Done! pass1 - making usageList (622 chroms): 2 millis pass2 - checking and writing primary data (3010 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:06:26: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:06:33: 9000000 INFO @ Sun, 21 Jun 2020 18:06:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:06:40: 10000000 INFO @ Sun, 21 Jun 2020 18:06:40: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:06:40: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:06:40: #1 total tags in treatment: 10026461 INFO @ Sun, 21 Jun 2020 18:06:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:40: #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 18:06:41: #1 tags after filtering in treatment: 10026345 INFO @ Sun, 21 Jun 2020 18:06:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:41: #2 number of paired peaks: 2557 INFO @ Sun, 21 Jun 2020 18:06:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:41: #2 predicted fragment length is 108 bps INFO @ Sun, 21 Jun 2020 18:06:41: #2 alternative fragment length(s) may be 3,108 bps INFO @ Sun, 21 Jun 2020 18:06:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.20_model.r WARNING @ Sun, 21 Jun 2020 18:06:41: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:06:41: #2 You may need to consider one of the other alternative d(s): 3,108 WARNING @ Sun, 21 Jun 2020 18:06:41: #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 18:06:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.10_summits.bed INFO @ Sun, 21 Jun 2020 18:06:48: Done! pass1 - making usageList (563 chroms): 1 millis pass2 - checking and writing primary data (1845 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:07:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1158170/SRX1158170.20_summits.bed INFO @ Sun, 21 Jun 2020 18:07:13: Done! pass1 - making usageList (466 chroms): 1 millis pass2 - checking and writing primary data (1037 records, 4 fields): 14 millis CompletedMACS2peakCalling