Job ID = 6455720 SRX = SRX288017 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:14:06 prefetch.2.10.7: 1) Downloading 'SRR870206'... 2020-06-21T10:14:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:17:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:17:54 prefetch.2.10.7: 'SRR870206' is valid 2020-06-21T10:17:54 prefetch.2.10.7: 1) 'SRR870206' was downloaded successfully Read 15256806 spots for SRR870206/SRR870206.sra Written 15256806 spots for SRR870206/SRR870206.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:09 15256806 reads; of these: 15256806 (100.00%) were unpaired; of these: 838339 (5.49%) aligned 0 times 10144942 (66.49%) aligned exactly 1 time 4273525 (28.01%) aligned >1 times 94.51% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 1924802 / 14418467 = 0.1335 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 19:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.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 19:26:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:45: 1000000 INFO @ Sun, 21 Jun 2020 19:26:50: 2000000 INFO @ Sun, 21 Jun 2020 19:26:56: 3000000 INFO @ Sun, 21 Jun 2020 19:27:01: 4000000 INFO @ Sun, 21 Jun 2020 19:27:07: 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 19:27:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.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 19:27:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:12: 6000000 INFO @ Sun, 21 Jun 2020 19:27:14: 1000000 INFO @ Sun, 21 Jun 2020 19:27:18: 7000000 INFO @ Sun, 21 Jun 2020 19:27:19: 2000000 INFO @ Sun, 21 Jun 2020 19:27:24: 8000000 INFO @ Sun, 21 Jun 2020 19:27:24: 3000000 INFO @ Sun, 21 Jun 2020 19:27:29: 4000000 INFO @ Sun, 21 Jun 2020 19:27:29: 9000000 INFO @ Sun, 21 Jun 2020 19:27:34: 5000000 INFO @ Sun, 21 Jun 2020 19:27:35: 10000000 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 19:27:39: 6000000 INFO @ Sun, 21 Jun 2020 19:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.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 19:27:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:41: 11000000 INFO @ Sun, 21 Jun 2020 19:27:44: 7000000 INFO @ Sun, 21 Jun 2020 19:27:45: 1000000 INFO @ Sun, 21 Jun 2020 19:27:47: 12000000 INFO @ Sun, 21 Jun 2020 19:27:49: 8000000 INFO @ Sun, 21 Jun 2020 19:27:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:50: #1 total tags in treatment: 12493665 INFO @ Sun, 21 Jun 2020 19:27:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:50: #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 19:27:51: #1 tags after filtering in treatment: 12493665 INFO @ Sun, 21 Jun 2020 19:27:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:51: 2000000 INFO @ Sun, 21 Jun 2020 19:27:52: #2 number of paired peaks: 1482 INFO @ Sun, 21 Jun 2020 19:27:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:52: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 19:27:52: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 19:27:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.05_model.r INFO @ Sun, 21 Jun 2020 19:27:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:54: 9000000 INFO @ Sun, 21 Jun 2020 19:27:57: 3000000 INFO @ Sun, 21 Jun 2020 19:27:58: 10000000 INFO @ Sun, 21 Jun 2020 19:28:03: 4000000 INFO @ Sun, 21 Jun 2020 19:28:04: 11000000 INFO @ Sun, 21 Jun 2020 19:28:08: 5000000 INFO @ Sun, 21 Jun 2020 19:28:09: 12000000 INFO @ Sun, 21 Jun 2020 19:28:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:12: #1 total tags in treatment: 12493665 INFO @ Sun, 21 Jun 2020 19:28:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:12: #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 19:28:12: #1 tags after filtering in treatment: 12493665 INFO @ Sun, 21 Jun 2020 19:28:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:13: #2 number of paired peaks: 1482 INFO @ Sun, 21 Jun 2020 19:28:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:13: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 19:28:13: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 19:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.10_model.r INFO @ Sun, 21 Jun 2020 19:28:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:14: 6000000 INFO @ Sun, 21 Jun 2020 19:28:20: 7000000 INFO @ Sun, 21 Jun 2020 19:28:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:25: 8000000 INFO @ Sun, 21 Jun 2020 19:28:31: 9000000 INFO @ Sun, 21 Jun 2020 19:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.05_summits.bed INFO @ Sun, 21 Jun 2020 19:28:35: Done! pass1 - making usageList (705 chroms): 1 millis pass2 - checking and writing primary data (4880 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:36: 10000000 INFO @ Sun, 21 Jun 2020 19:28:42: 11000000 INFO @ Sun, 21 Jun 2020 19:28:42: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:28:48: 12000000 INFO @ Sun, 21 Jun 2020 19:28:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:51: #1 total tags in treatment: 12493665 INFO @ Sun, 21 Jun 2020 19:28:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:51: #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 19:28:51: #1 tags after filtering in treatment: 12493665 INFO @ Sun, 21 Jun 2020 19:28:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:52: #2 number of paired peaks: 1482 INFO @ Sun, 21 Jun 2020 19:28:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:52: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 19:28:52: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 19:28:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.20_model.r INFO @ Sun, 21 Jun 2020 19:28:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.10_summits.bed INFO @ Sun, 21 Jun 2020 19:28:56: Done! pass1 - making usageList (568 chroms): 2 millis pass2 - checking and writing primary data (3379 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:29:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288017/SRX288017.20_summits.bed INFO @ Sun, 21 Jun 2020 19:29:36: Done! pass1 - making usageList (450 chroms): 1 millis pass2 - checking and writing primary data (2253 records, 4 fields): 14 millis CompletedMACS2peakCalling