Job ID = 6453925 SRX = SRX1600295 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:59:19 prefetch.2.10.7: 1) Downloading 'SRR3187787'... 2020-06-21T08:59:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:04:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:04:26 prefetch.2.10.7: 1) 'SRR3187787' was downloaded successfully Read 23384087 spots for SRR3187787/SRR3187787.sra Written 23384087 spots for SRR3187787/SRR3187787.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: 00:06:17 23384087 reads; of these: 23384087 (100.00%) were unpaired; of these: 4347869 (18.59%) aligned 0 times 17324941 (74.09%) aligned exactly 1 time 1711277 (7.32%) aligned >1 times 81.41% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 10029865 / 19036218 = 0.5269 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 18:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.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 18:19:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:07: 1000000 INFO @ Sun, 21 Jun 2020 18:19:13: 2000000 INFO @ Sun, 21 Jun 2020 18:19:19: 3000000 INFO @ Sun, 21 Jun 2020 18:19:26: 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 18:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.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 18:19:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:32: 5000000 INFO @ Sun, 21 Jun 2020 18:19:37: 1000000 INFO @ Sun, 21 Jun 2020 18:19:39: 6000000 INFO @ Sun, 21 Jun 2020 18:19:44: 2000000 INFO @ Sun, 21 Jun 2020 18:19:46: 7000000 INFO @ Sun, 21 Jun 2020 18:19:50: 3000000 INFO @ Sun, 21 Jun 2020 18:19:54: 8000000 INFO @ Sun, 21 Jun 2020 18:19:57: 4000000 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 18:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.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 18:20:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:01: 9000000 INFO @ Sun, 21 Jun 2020 18:20:02: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:20:02: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:20:02: #1 total tags in treatment: 9006353 INFO @ Sun, 21 Jun 2020 18:20:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:02: #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 18:20:02: #1 tags after filtering in treatment: 9006326 INFO @ Sun, 21 Jun 2020 18:20:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:03: #2 number of paired peaks: 6970 INFO @ Sun, 21 Jun 2020 18:20:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:04: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 18:20:04: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 21 Jun 2020 18:20:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.05_model.r WARNING @ Sun, 21 Jun 2020 18:20:04: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:04: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sun, 21 Jun 2020 18:20:04: #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 18:20:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:04: 5000000 INFO @ Sun, 21 Jun 2020 18:20:08: 1000000 INFO @ Sun, 21 Jun 2020 18:20:11: 6000000 INFO @ Sun, 21 Jun 2020 18:20:16: 2000000 INFO @ Sun, 21 Jun 2020 18:20:19: 7000000 INFO @ Sun, 21 Jun 2020 18:20:23: 3000000 INFO @ Sun, 21 Jun 2020 18:20:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:27: 8000000 INFO @ Sun, 21 Jun 2020 18:20:31: 4000000 INFO @ Sun, 21 Jun 2020 18:20:35: 9000000 INFO @ Sun, 21 Jun 2020 18:20:36: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:20:36: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:20:36: #1 total tags in treatment: 9006353 INFO @ Sun, 21 Jun 2020 18:20:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:36: #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 18:20:36: #1 tags after filtering in treatment: 9006326 INFO @ Sun, 21 Jun 2020 18:20:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.05_summits.bed INFO @ Sun, 21 Jun 2020 18:20:37: Done! INFO @ Sun, 21 Jun 2020 18:20:37: #2 number of paired peaks: 6970 INFO @ Sun, 21 Jun 2020 18:20:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:38: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 18:20:38: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 21 Jun 2020 18:20:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.10_model.r WARNING @ Sun, 21 Jun 2020 18:20:38: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:38: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sun, 21 Jun 2020 18:20:38: #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 18:20:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:38: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (176 chroms): 3 millis pass2 - checking and writing primary data (9964 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:20:39: 5000000 INFO @ Sun, 21 Jun 2020 18:20:46: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:54: 7000000 INFO @ Sun, 21 Jun 2020 18:20:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:03: 8000000 INFO @ Sun, 21 Jun 2020 18:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:11: Done! pass1 - making usageList (117 chroms): 2 millis pass2 - checking and writing primary data (7881 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:12: 9000000 INFO @ Sun, 21 Jun 2020 18:21:12: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:21:12: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:21:12: #1 total tags in treatment: 9006353 INFO @ Sun, 21 Jun 2020 18:21:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:12: #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 18:21:13: #1 tags after filtering in treatment: 9006326 INFO @ Sun, 21 Jun 2020 18:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:14: #2 number of paired peaks: 6970 INFO @ Sun, 21 Jun 2020 18:21:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:14: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 18:21:14: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 21 Jun 2020 18:21:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.20_model.r WARNING @ Sun, 21 Jun 2020 18:21:14: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:14: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sun, 21 Jun 2020 18:21:14: #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 18:21:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1600295/SRX1600295.20_summits.bed INFO @ Sun, 21 Jun 2020 18:21:47: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (4429 records, 4 fields): 18 millis CompletedMACS2peakCalling