Job ID = 6454411 SRX = SRX2055943 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:03:19 prefetch.2.10.7: 1) Downloading 'SRR4069175'... 2020-06-21T09:03:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:04:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:04:46 prefetch.2.10.7: 'SRR4069175' is valid 2020-06-21T09:04:46 prefetch.2.10.7: 1) 'SRR4069175' was downloaded successfully Read 20989662 spots for SRR4069175/SRR4069175.sra Written 20989662 spots for SRR4069175/SRR4069175.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: 00:06:29 20989662 reads; of these: 20989662 (100.00%) were unpaired; of these: 8454374 (40.28%) aligned 0 times 7369820 (35.11%) aligned exactly 1 time 5165468 (24.61%) aligned >1 times 59.72% overall alignment rate Time searching: 00:06:29 Overall time: 00:06:29 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] 3976457 / 12535288 = 0.3172 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 18:15:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.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 18:15:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:27: 1000000 INFO @ Sun, 21 Jun 2020 18:15:33: 2000000 INFO @ Sun, 21 Jun 2020 18:15:39: 3000000 INFO @ Sun, 21 Jun 2020 18:15:44: 4000000 INFO @ Sun, 21 Jun 2020 18:15:50: 5000000 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 18:15:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.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 18:15:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:56: 6000000 INFO @ Sun, 21 Jun 2020 18:15:58: 1000000 INFO @ Sun, 21 Jun 2020 18:16:03: 7000000 INFO @ Sun, 21 Jun 2020 18:16:05: 2000000 INFO @ Sun, 21 Jun 2020 18:16:10: 8000000 INFO @ Sun, 21 Jun 2020 18:16:11: 3000000 INFO @ Sun, 21 Jun 2020 18:16:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:16:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:16:13: #1 total tags in treatment: 8558831 INFO @ Sun, 21 Jun 2020 18:16:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:13: #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 18:16:14: #1 tags after filtering in treatment: 8558735 INFO @ Sun, 21 Jun 2020 18:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:15: #2 number of paired peaks: 2677 INFO @ Sun, 21 Jun 2020 18:16:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:15: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 18:16:15: #2 alternative fragment length(s) may be 4,103 bps INFO @ Sun, 21 Jun 2020 18:16:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.05_model.r INFO @ Sun, 21 Jun 2020 18:16:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:16:18: 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 18:16:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.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 18:16:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:24: 5000000 INFO @ Sun, 21 Jun 2020 18:16:28: 1000000 INFO @ Sun, 21 Jun 2020 18:16:30: 6000000 INFO @ Sun, 21 Jun 2020 18:16:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:35: 2000000 INFO @ Sun, 21 Jun 2020 18:16:37: 7000000 INFO @ Sun, 21 Jun 2020 18:16:41: 3000000 INFO @ Sun, 21 Jun 2020 18:16:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.05_summits.bed INFO @ Sun, 21 Jun 2020 18:16:43: Done! pass1 - making usageList (641 chroms): 1 millis pass2 - checking and writing primary data (3233 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:16:44: 8000000 INFO @ Sun, 21 Jun 2020 18:16:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:16:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:16:48: #1 total tags in treatment: 8558831 INFO @ Sun, 21 Jun 2020 18:16:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:48: #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 18:16:48: 4000000 INFO @ Sun, 21 Jun 2020 18:16:48: #1 tags after filtering in treatment: 8558735 INFO @ Sun, 21 Jun 2020 18:16:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:49: #2 number of paired peaks: 2677 INFO @ Sun, 21 Jun 2020 18:16:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:49: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 18:16:49: #2 alternative fragment length(s) may be 4,103 bps INFO @ Sun, 21 Jun 2020 18:16:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.10_model.r INFO @ Sun, 21 Jun 2020 18:16:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:16:54: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:17:00: 6000000 INFO @ Sun, 21 Jun 2020 18:17:06: 7000000 INFO @ Sun, 21 Jun 2020 18:17:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:12: 8000000 INFO @ Sun, 21 Jun 2020 18:17:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:17:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:17:15: #1 total tags in treatment: 8558831 INFO @ Sun, 21 Jun 2020 18:17:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:15: #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 18:17:16: #1 tags after filtering in treatment: 8558735 INFO @ Sun, 21 Jun 2020 18:17:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:16: #2 number of paired peaks: 2677 INFO @ Sun, 21 Jun 2020 18:17:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:16: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 18:17:16: #2 alternative fragment length(s) may be 4,103 bps INFO @ Sun, 21 Jun 2020 18:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.20_model.r INFO @ Sun, 21 Jun 2020 18:17:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:17:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.10_summits.bed INFO @ Sun, 21 Jun 2020 18:17:18: Done! pass1 - making usageList (523 chroms): 1 millis pass2 - checking and writing primary data (2102 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:17:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055943/SRX2055943.20_summits.bed INFO @ Sun, 21 Jun 2020 18:17:44: Done! pass1 - making usageList (430 chroms): 1 millis pass2 - checking and writing primary data (1333 records, 4 fields): 13 millis CompletedMACS2peakCalling