Job ID = 6453354 SRX = SRX1120689 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:08:18 prefetch.2.10.7: 1) Downloading 'SRR2129921'... 2020-06-21T08:08:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:12:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:12:32 prefetch.2.10.7: 1) 'SRR2129921' was downloaded successfully Read 13160753 spots for SRR2129921/SRR2129921.sra Written 13160753 spots for SRR2129921/SRR2129921.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: 00:06:09 13160753 reads; of these: 13160753 (100.00%) were unpaired; of these: 813267 (6.18%) aligned 0 times 4099192 (31.15%) aligned exactly 1 time 8248294 (62.67%) aligned >1 times 93.82% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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] 4071443 / 12347486 = 0.3297 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 17:23:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.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 17:23:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:35: 1000000 INFO @ Sun, 21 Jun 2020 17:23:43: 2000000 INFO @ Sun, 21 Jun 2020 17:23:51: 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 17:23:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.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 17:23:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:00: 4000000 INFO @ Sun, 21 Jun 2020 17:24:06: 1000000 INFO @ Sun, 21 Jun 2020 17:24:09: 5000000 INFO @ Sun, 21 Jun 2020 17:24:15: 2000000 INFO @ Sun, 21 Jun 2020 17:24:18: 6000000 INFO @ Sun, 21 Jun 2020 17:24:24: 3000000 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 17:24:27: 7000000 INFO @ Sun, 21 Jun 2020 17:24:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.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 17:24:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:33: 4000000 INFO @ Sun, 21 Jun 2020 17:24:36: 1000000 INFO @ Sun, 21 Jun 2020 17:24:36: 8000000 INFO @ Sun, 21 Jun 2020 17:24:39: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:24:39: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:24:39: #1 total tags in treatment: 8276043 INFO @ Sun, 21 Jun 2020 17:24:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:39: #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 17:24:39: #1 tags after filtering in treatment: 8275969 INFO @ Sun, 21 Jun 2020 17:24:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:40: #2 number of paired peaks: 4990 INFO @ Sun, 21 Jun 2020 17:24:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:40: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:40: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:40: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:40: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 17:24:40: #2 alternative fragment length(s) may be 3,87 bps INFO @ Sun, 21 Jun 2020 17:24:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.05_model.r WARNING @ Sun, 21 Jun 2020 17:24:40: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:24:40: #2 You may need to consider one of the other alternative d(s): 3,87 WARNING @ Sun, 21 Jun 2020 17:24:40: #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 17:24:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:24:42: 5000000 INFO @ Sun, 21 Jun 2020 17:24:44: 2000000 INFO @ Sun, 21 Jun 2020 17:24:51: 6000000 INFO @ Sun, 21 Jun 2020 17:24:52: 3000000 INFO @ Sun, 21 Jun 2020 17:24:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:25:00: 4000000 INFO @ Sun, 21 Jun 2020 17:25:00: 7000000 INFO @ Sun, 21 Jun 2020 17:25:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:25:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:25:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.05_summits.bed INFO @ Sun, 21 Jun 2020 17:25:04: Done! pass1 - making usageList (952 chroms): 1 millis pass2 - checking and writing primary data (3695 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:25:08: 5000000 INFO @ Sun, 21 Jun 2020 17:25:09: 8000000 INFO @ Sun, 21 Jun 2020 17:25:12: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:25:12: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:25:12: #1 total tags in treatment: 8276043 INFO @ Sun, 21 Jun 2020 17:25:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:25:12: #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 17:25:12: #1 tags after filtering in treatment: 8275969 INFO @ Sun, 21 Jun 2020 17:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:12: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:13: #2 number of paired peaks: 4990 INFO @ Sun, 21 Jun 2020 17:25:13: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:13: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:13: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:13: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:13: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 17:25:13: #2 alternative fragment length(s) may be 3,87 bps INFO @ Sun, 21 Jun 2020 17:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.10_model.r WARNING @ Sun, 21 Jun 2020 17:25:13: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:25:13: #2 You may need to consider one of the other alternative d(s): 3,87 WARNING @ Sun, 21 Jun 2020 17:25:13: #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 17:25:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:25:16: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:25:23: 7000000 INFO @ Sun, 21 Jun 2020 17:25:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:25:30: 8000000 INFO @ Sun, 21 Jun 2020 17:25:32: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:25:32: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:25:32: #1 total tags in treatment: 8276043 INFO @ Sun, 21 Jun 2020 17:25:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:25:32: #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 17:25:32: #1 tags after filtering in treatment: 8275969 INFO @ Sun, 21 Jun 2020 17:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:33: #2 number of paired peaks: 4990 INFO @ Sun, 21 Jun 2020 17:25:33: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:33: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:33: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:33: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:33: #2 predicted fragment length is 87 bps INFO @ Sun, 21 Jun 2020 17:25:33: #2 alternative fragment length(s) may be 3,87 bps INFO @ Sun, 21 Jun 2020 17:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.20_model.r WARNING @ Sun, 21 Jun 2020 17:25:33: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:25:33: #2 You may need to consider one of the other alternative d(s): 3,87 WARNING @ Sun, 21 Jun 2020 17:25:33: #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 17:25:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:25:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:25:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:25:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.10_summits.bed INFO @ Sun, 21 Jun 2020 17:25:37: Done! pass1 - making usageList (750 chroms): 1 millis pass2 - checking and writing primary data (2113 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:25:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120689/SRX1120689.20_summits.bed INFO @ Sun, 21 Jun 2020 17:25:57: Done! pass1 - making usageList (574 chroms): 2 millis pass2 - checking and writing primary data (1386 records, 4 fields): 15 millis CompletedMACS2peakCalling