Job ID = 6498055 SRX = SRX297097 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:55:58 prefetch.2.10.7: 1) Downloading 'SRR886298'... 2020-06-25T22:55:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:58:55 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:58:55 prefetch.2.10.7: 1) 'SRR886298' was downloaded successfully Read 28354404 spots for SRR886298/SRR886298.sra Written 28354404 spots for SRR886298/SRR886298.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: 00:14:37 28354404 reads; of these: 28354404 (100.00%) were unpaired; of these: 1462593 (5.16%) aligned 0 times 13070951 (46.10%) aligned exactly 1 time 13820860 (48.74%) aligned >1 times 94.84% overall alignment rate Time searching: 00:14:37 Overall time: 00:14:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 14533920 / 26891811 = 0.5405 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 @ Fri, 26 Jun 2020 08:21:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.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 @ Fri, 26 Jun 2020 08:21:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:21:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:21:48: 1000000 INFO @ Fri, 26 Jun 2020 08:21:54: 2000000 INFO @ Fri, 26 Jun 2020 08:22:00: 3000000 INFO @ Fri, 26 Jun 2020 08:22:06: 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 @ Fri, 26 Jun 2020 08:22:12: 5000000 INFO @ Fri, 26 Jun 2020 08:22:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.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 @ Fri, 26 Jun 2020 08:22:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:22:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:22:18: 6000000 INFO @ Fri, 26 Jun 2020 08:22:19: 1000000 INFO @ Fri, 26 Jun 2020 08:22:25: 7000000 INFO @ Fri, 26 Jun 2020 08:22:25: 2000000 INFO @ Fri, 26 Jun 2020 08:22:32: 8000000 INFO @ Fri, 26 Jun 2020 08:22:32: 3000000 INFO @ Fri, 26 Jun 2020 08:22:38: 9000000 INFO @ Fri, 26 Jun 2020 08:22:39: 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 @ Fri, 26 Jun 2020 08:22:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.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 @ Fri, 26 Jun 2020 08:22:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:22:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:22:45: 10000000 INFO @ Fri, 26 Jun 2020 08:22:46: 5000000 INFO @ Fri, 26 Jun 2020 08:22:49: 1000000 INFO @ Fri, 26 Jun 2020 08:22:52: 11000000 INFO @ Fri, 26 Jun 2020 08:22:53: 6000000 INFO @ Fri, 26 Jun 2020 08:22:55: 2000000 INFO @ Fri, 26 Jun 2020 08:22:58: 12000000 INFO @ Fri, 26 Jun 2020 08:23:00: 7000000 INFO @ Fri, 26 Jun 2020 08:23:01: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:23:01: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:23:01: #1 total tags in treatment: 12357891 INFO @ Fri, 26 Jun 2020 08:23:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:23:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:23:01: #1 tags after filtering in treatment: 12357891 INFO @ Fri, 26 Jun 2020 08:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:23:01: #1 finished! INFO @ Fri, 26 Jun 2020 08:23:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:23:02: 3000000 INFO @ Fri, 26 Jun 2020 08:23:02: #2 number of paired peaks: 4414 INFO @ Fri, 26 Jun 2020 08:23:02: start model_add_line... INFO @ Fri, 26 Jun 2020 08:23:02: start X-correlation... INFO @ Fri, 26 Jun 2020 08:23:03: end of X-cor INFO @ Fri, 26 Jun 2020 08:23:03: #2 finished! INFO @ Fri, 26 Jun 2020 08:23:03: #2 predicted fragment length is 105 bps INFO @ Fri, 26 Jun 2020 08:23:03: #2 alternative fragment length(s) may be 105 bps INFO @ Fri, 26 Jun 2020 08:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.05_model.r INFO @ Fri, 26 Jun 2020 08:23:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:23:07: 8000000 INFO @ Fri, 26 Jun 2020 08:23:09: 4000000 INFO @ Fri, 26 Jun 2020 08:23:14: 9000000 INFO @ Fri, 26 Jun 2020 08:23:15: 5000000 INFO @ Fri, 26 Jun 2020 08:23:21: 10000000 INFO @ Fri, 26 Jun 2020 08:23:22: 6000000 INFO @ Fri, 26 Jun 2020 08:23:29: 11000000 INFO @ Fri, 26 Jun 2020 08:23:29: 7000000 INFO @ Fri, 26 Jun 2020 08:23:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:23:36: 12000000 INFO @ Fri, 26 Jun 2020 08:23:36: 8000000 INFO @ Fri, 26 Jun 2020 08:23:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:23:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:23:38: #1 total tags in treatment: 12357891 INFO @ Fri, 26 Jun 2020 08:23:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:23:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:23:39: #1 tags after filtering in treatment: 12357891 INFO @ Fri, 26 Jun 2020 08:23:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:23:39: #1 finished! INFO @ Fri, 26 Jun 2020 08:23:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:23:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:23:40: #2 number of paired peaks: 4414 INFO @ Fri, 26 Jun 2020 08:23:40: start model_add_line... INFO @ Fri, 26 Jun 2020 08:23:40: start X-correlation... INFO @ Fri, 26 Jun 2020 08:23:40: end of X-cor INFO @ Fri, 26 Jun 2020 08:23:40: #2 finished! INFO @ Fri, 26 Jun 2020 08:23:40: #2 predicted fragment length is 105 bps INFO @ Fri, 26 Jun 2020 08:23:40: #2 alternative fragment length(s) may be 105 bps INFO @ Fri, 26 Jun 2020 08:23:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.10_model.r INFO @ Fri, 26 Jun 2020 08:23:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:23:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:23:42: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:23:49: 10000000 INFO @ Fri, 26 Jun 2020 08:23:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:23:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:23:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.05_summits.bed INFO @ Fri, 26 Jun 2020 08:23:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (19130 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:23:55: 11000000 INFO @ Fri, 26 Jun 2020 08:24:01: 12000000 INFO @ Fri, 26 Jun 2020 08:24:03: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:24:03: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:24:03: #1 total tags in treatment: 12357891 INFO @ Fri, 26 Jun 2020 08:24:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:24:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:24:03: #1 tags after filtering in treatment: 12357891 INFO @ Fri, 26 Jun 2020 08:24:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:24:03: #1 finished! INFO @ Fri, 26 Jun 2020 08:24:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:24:05: #2 number of paired peaks: 4414 INFO @ Fri, 26 Jun 2020 08:24:05: start model_add_line... INFO @ Fri, 26 Jun 2020 08:24:05: start X-correlation... INFO @ Fri, 26 Jun 2020 08:24:05: end of X-cor INFO @ Fri, 26 Jun 2020 08:24:05: #2 finished! INFO @ Fri, 26 Jun 2020 08:24:05: #2 predicted fragment length is 105 bps INFO @ Fri, 26 Jun 2020 08:24:05: #2 alternative fragment length(s) may be 105 bps INFO @ Fri, 26 Jun 2020 08:24:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.20_model.r INFO @ Fri, 26 Jun 2020 08:24:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:24:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:24:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:24:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:24:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:24:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.10_summits.bed INFO @ Fri, 26 Jun 2020 08:24:29: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (15139 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:24:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:24:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:24:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX297097/SRX297097.20_summits.bed INFO @ Fri, 26 Jun 2020 08:24:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7276 records, 4 fields): 10 millis CompletedMACS2peakCalling