Job ID = 6498035 SRX = SRX287908 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:11:33 prefetch.2.10.7: 1) Downloading 'SRR870097'... 2020-06-25T23:11:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:13:38 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:13:39 prefetch.2.10.7: 'SRR870097' is valid 2020-06-25T23:13:39 prefetch.2.10.7: 1) 'SRR870097' was downloaded successfully Read 14137955 spots for SRR870097/SRR870097.sra Written 14137955 spots for SRR870097/SRR870097.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: 00:03:38 14137955 reads; of these: 14137955 (100.00%) were unpaired; of these: 1100372 (7.78%) aligned 0 times 11324648 (80.10%) aligned exactly 1 time 1712935 (12.12%) aligned >1 times 92.22% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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 8 files... [bam_rmdupse_core] 2549336 / 13037583 = 0.1955 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 08:21:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.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 08:21:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:21:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:21:57: 1000000 INFO @ Fri, 26 Jun 2020 08:22:03: 2000000 INFO @ Fri, 26 Jun 2020 08:22:09: 3000000 INFO @ Fri, 26 Jun 2020 08:22:15: 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 08:22:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.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 08:22:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:22:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:22:21: 5000000 INFO @ Fri, 26 Jun 2020 08:22:27: 1000000 INFO @ Fri, 26 Jun 2020 08:22:27: 6000000 INFO @ Fri, 26 Jun 2020 08:22:33: 2000000 INFO @ Fri, 26 Jun 2020 08:22:33: 7000000 INFO @ Fri, 26 Jun 2020 08:22:39: 3000000 INFO @ Fri, 26 Jun 2020 08:22:39: 8000000 INFO @ Fri, 26 Jun 2020 08:22:45: 4000000 INFO @ Fri, 26 Jun 2020 08:22:46: 9000000 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 08:22:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.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 08:22:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:22:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:22:51: 5000000 INFO @ Fri, 26 Jun 2020 08:22:52: 10000000 INFO @ Fri, 26 Jun 2020 08:22:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:22:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:22:55: #1 total tags in treatment: 10488247 INFO @ Fri, 26 Jun 2020 08:22:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:22:55: #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 08:22:55: #1 tags after filtering in treatment: 10488247 INFO @ Fri, 26 Jun 2020 08:22:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:22:55: #1 finished! INFO @ Fri, 26 Jun 2020 08:22:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:22:56: #2 number of paired peaks: 3709 INFO @ Fri, 26 Jun 2020 08:22:56: start model_add_line... INFO @ Fri, 26 Jun 2020 08:22:56: start X-correlation... INFO @ Fri, 26 Jun 2020 08:22:56: end of X-cor INFO @ Fri, 26 Jun 2020 08:22:56: #2 finished! INFO @ Fri, 26 Jun 2020 08:22:56: #2 predicted fragment length is 198 bps INFO @ Fri, 26 Jun 2020 08:22:56: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 26 Jun 2020 08:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.05_model.r INFO @ Fri, 26 Jun 2020 08:22:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:22:57: 1000000 INFO @ Fri, 26 Jun 2020 08:22:57: 6000000 INFO @ Fri, 26 Jun 2020 08:23:03: 2000000 INFO @ Fri, 26 Jun 2020 08:23:04: 7000000 INFO @ Fri, 26 Jun 2020 08:23:10: 3000000 INFO @ Fri, 26 Jun 2020 08:23:10: 8000000 INFO @ Fri, 26 Jun 2020 08:23:16: 4000000 INFO @ Fri, 26 Jun 2020 08:23:16: 9000000 INFO @ Fri, 26 Jun 2020 08:23:22: 5000000 INFO @ Fri, 26 Jun 2020 08:23:22: 10000000 INFO @ Fri, 26 Jun 2020 08:23:25: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:23:25: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:23:25: #1 total tags in treatment: 10488247 INFO @ Fri, 26 Jun 2020 08:23:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:23:25: #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 08:23:26: #1 tags after filtering in treatment: 10488247 INFO @ Fri, 26 Jun 2020 08:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:23:26: #1 finished! INFO @ Fri, 26 Jun 2020 08:23:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:23:27: #2 number of paired peaks: 3709 INFO @ Fri, 26 Jun 2020 08:23:27: start model_add_line... INFO @ Fri, 26 Jun 2020 08:23:27: start X-correlation... INFO @ Fri, 26 Jun 2020 08:23:27: end of X-cor INFO @ Fri, 26 Jun 2020 08:23:27: #2 finished! INFO @ Fri, 26 Jun 2020 08:23:27: #2 predicted fragment length is 198 bps INFO @ Fri, 26 Jun 2020 08:23:27: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 26 Jun 2020 08:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.10_model.r INFO @ Fri, 26 Jun 2020 08:23:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:23:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:23:28: 6000000 INFO @ Fri, 26 Jun 2020 08:23:34: 7000000 INFO @ Fri, 26 Jun 2020 08:23:41: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.05_summits.bed INFO @ Fri, 26 Jun 2020 08:23:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8286 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:23:47: 9000000 INFO @ Fri, 26 Jun 2020 08:23:53: 10000000 INFO @ Fri, 26 Jun 2020 08:23:56: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:23:56: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:23:56: #1 total tags in treatment: 10488247 INFO @ Fri, 26 Jun 2020 08:23:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:23:56: #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 08:23:56: #1 tags after filtering in treatment: 10488247 INFO @ Fri, 26 Jun 2020 08:23:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:23:56: #1 finished! INFO @ Fri, 26 Jun 2020 08:23:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:23:57: #2 number of paired peaks: 3709 INFO @ Fri, 26 Jun 2020 08:23:57: start model_add_line... INFO @ Fri, 26 Jun 2020 08:23:57: start X-correlation... INFO @ Fri, 26 Jun 2020 08:23:57: end of X-cor INFO @ Fri, 26 Jun 2020 08:23:57: #2 finished! INFO @ Fri, 26 Jun 2020 08:23:57: #2 predicted fragment length is 198 bps INFO @ Fri, 26 Jun 2020 08:23:57: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 26 Jun 2020 08:23:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.20_model.r INFO @ Fri, 26 Jun 2020 08:23:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:23:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:23:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:24:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:24:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:24:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.10_summits.bed INFO @ Fri, 26 Jun 2020 08:24:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6643 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:24:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:24:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:24:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:24:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287908/SRX287908.20_summits.bed INFO @ Fri, 26 Jun 2020 08:24:45: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4873 records, 4 fields): 6 millis CompletedMACS2peakCalling