Job ID = 6626978 SRX = SRX7974997 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T00:07:33 prefetch.2.10.7: 1) Downloading 'SRR11396282'... 2020-07-14T00:07:33 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:09:37 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:09:37 prefetch.2.10.7: 1) 'SRR11396282' was downloaded successfully Read 23623005 spots for SRR11396282/SRR11396282.sra Written 23623005 spots for SRR11396282/SRR11396282.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627118 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:10 23623005 reads; of these: 23623005 (100.00%) were unpaired; of these: 7202850 (30.49%) aligned 0 times 15102129 (63.93%) aligned exactly 1 time 1318026 (5.58%) aligned >1 times 69.51% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 3901060 / 16420155 = 0.2376 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 @ Tue, 14 Jul 2020 09:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.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 @ Tue, 14 Jul 2020 09:19:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:19:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:19:12: 1000000 INFO @ Tue, 14 Jul 2020 09:19:18: 2000000 INFO @ Tue, 14 Jul 2020 09:19:24: 3000000 INFO @ Tue, 14 Jul 2020 09:19:31: 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 @ Tue, 14 Jul 2020 09:19:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.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 @ Tue, 14 Jul 2020 09:19:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:19:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:19:37: 5000000 INFO @ Tue, 14 Jul 2020 09:19:42: 1000000 INFO @ Tue, 14 Jul 2020 09:19:43: 6000000 INFO @ Tue, 14 Jul 2020 09:19:48: 2000000 INFO @ Tue, 14 Jul 2020 09:19:50: 7000000 INFO @ Tue, 14 Jul 2020 09:19:53: 3000000 INFO @ Tue, 14 Jul 2020 09:19:56: 8000000 INFO @ Tue, 14 Jul 2020 09:19:59: 4000000 INFO @ Tue, 14 Jul 2020 09:20:03: 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 @ Tue, 14 Jul 2020 09:20:05: 5000000 INFO @ Tue, 14 Jul 2020 09:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.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 @ Tue, 14 Jul 2020 09:20:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:20:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:20:09: 10000000 INFO @ Tue, 14 Jul 2020 09:20:11: 6000000 INFO @ Tue, 14 Jul 2020 09:20:12: 1000000 INFO @ Tue, 14 Jul 2020 09:20:16: 11000000 INFO @ Tue, 14 Jul 2020 09:20:17: 7000000 INFO @ Tue, 14 Jul 2020 09:20:19: 2000000 INFO @ Tue, 14 Jul 2020 09:20:22: 12000000 INFO @ Tue, 14 Jul 2020 09:20:23: 8000000 INFO @ Tue, 14 Jul 2020 09:20:25: 3000000 INFO @ Tue, 14 Jul 2020 09:20:26: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:20:26: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:20:26: #1 total tags in treatment: 12519095 INFO @ Tue, 14 Jul 2020 09:20:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:20:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:20:26: #1 tags after filtering in treatment: 12519095 INFO @ Tue, 14 Jul 2020 09:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:20:26: #1 finished! INFO @ Tue, 14 Jul 2020 09:20:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:20:27: #2 number of paired peaks: 7067 INFO @ Tue, 14 Jul 2020 09:20:27: start model_add_line... INFO @ Tue, 14 Jul 2020 09:20:28: start X-correlation... INFO @ Tue, 14 Jul 2020 09:20:28: end of X-cor INFO @ Tue, 14 Jul 2020 09:20:28: #2 finished! INFO @ Tue, 14 Jul 2020 09:20:28: #2 predicted fragment length is 269 bps INFO @ Tue, 14 Jul 2020 09:20:28: #2 alternative fragment length(s) may be 269 bps INFO @ Tue, 14 Jul 2020 09:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.05_model.r INFO @ Tue, 14 Jul 2020 09:20:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:20:29: 9000000 INFO @ Tue, 14 Jul 2020 09:20:32: 4000000 INFO @ Tue, 14 Jul 2020 09:20:35: 10000000 INFO @ Tue, 14 Jul 2020 09:20:38: 5000000 INFO @ Tue, 14 Jul 2020 09:20:41: 11000000 INFO @ Tue, 14 Jul 2020 09:20:44: 6000000 INFO @ Tue, 14 Jul 2020 09:20:47: 12000000 INFO @ Tue, 14 Jul 2020 09:20:50: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:20:50: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:20:50: #1 total tags in treatment: 12519095 INFO @ Tue, 14 Jul 2020 09:20:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:20:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:20:50: #1 tags after filtering in treatment: 12519095 INFO @ Tue, 14 Jul 2020 09:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:20:50: #1 finished! INFO @ Tue, 14 Jul 2020 09:20:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:20:51: 7000000 INFO @ Tue, 14 Jul 2020 09:20:52: #2 number of paired peaks: 7067 INFO @ Tue, 14 Jul 2020 09:20:52: start model_add_line... INFO @ Tue, 14 Jul 2020 09:20:52: start X-correlation... INFO @ Tue, 14 Jul 2020 09:20:52: end of X-cor INFO @ Tue, 14 Jul 2020 09:20:52: #2 finished! INFO @ Tue, 14 Jul 2020 09:20:52: #2 predicted fragment length is 269 bps INFO @ Tue, 14 Jul 2020 09:20:52: #2 alternative fragment length(s) may be 269 bps INFO @ Tue, 14 Jul 2020 09:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.10_model.r INFO @ Tue, 14 Jul 2020 09:20:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:20:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:20:57: 8000000 INFO @ Tue, 14 Jul 2020 09:21:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:21:04: 9000000 INFO @ Tue, 14 Jul 2020 09:21:11: 10000000 INFO @ Tue, 14 Jul 2020 09:21:17: 11000000 INFO @ Tue, 14 Jul 2020 09:21:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:21:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:21:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.05_summits.bed INFO @ Tue, 14 Jul 2020 09:21:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (7227 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:21:23: 12000000 INFO @ Tue, 14 Jul 2020 09:21:27: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:21:27: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:21:27: #1 total tags in treatment: 12519095 INFO @ Tue, 14 Jul 2020 09:21:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:21:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:21:27: #1 tags after filtering in treatment: 12519095 INFO @ Tue, 14 Jul 2020 09:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:21:27: #1 finished! INFO @ Tue, 14 Jul 2020 09:21:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:21:28: #2 number of paired peaks: 7067 INFO @ Tue, 14 Jul 2020 09:21:28: start model_add_line... INFO @ Tue, 14 Jul 2020 09:21:28: start X-correlation... INFO @ Tue, 14 Jul 2020 09:21:28: end of X-cor INFO @ Tue, 14 Jul 2020 09:21:28: #2 finished! INFO @ Tue, 14 Jul 2020 09:21:28: #2 predicted fragment length is 269 bps INFO @ Tue, 14 Jul 2020 09:21:28: #2 alternative fragment length(s) may be 269 bps INFO @ Tue, 14 Jul 2020 09:21:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.20_model.r INFO @ Tue, 14 Jul 2020 09:21:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:21:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:21:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:21:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:21:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.10_summits.bed INFO @ Tue, 14 Jul 2020 09:21:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6161 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:22:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:22:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:22:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:22:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974997/SRX7974997.20_summits.bed INFO @ Tue, 14 Jul 2020 09:22:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5030 records, 4 fields): 7 millis CompletedMACS2peakCalling