Job ID = 6452620 SRX = SRX018632 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:51:17 prefetch.2.10.7: 1) Downloading 'SRR039103'... 2020-06-21T07:51:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:52:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:52:11 prefetch.2.10.7: 'SRR039103' is valid 2020-06-21T07:52:11 prefetch.2.10.7: 1) 'SRR039103' was downloaded successfully Read 5703341 spots for SRR039103/SRR039103.sra Written 5703341 spots for SRR039103/SRR039103.sra 2020-06-21T07:52:36 prefetch.2.10.7: 1) Downloading 'SRR039104'... 2020-06-21T07:52:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:53:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:53:49 prefetch.2.10.7: 'SRR039104' is valid 2020-06-21T07:53:49 prefetch.2.10.7: 1) 'SRR039104' was downloaded successfully Read 6070585 spots for SRR039104/SRR039104.sra Written 6070585 spots for SRR039104/SRR039104.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: 00:02:13 11773926 reads; of these: 11773926 (100.00%) were unpaired; of these: 3297728 (28.01%) aligned 0 times 6059473 (51.47%) aligned exactly 1 time 2416725 (20.53%) aligned >1 times 71.99% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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_rmdupse_core] 711459 / 8476198 = 0.0839 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 16:58:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.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 16:58:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:57: 1000000 INFO @ Sun, 21 Jun 2020 16:59:03: 2000000 INFO @ Sun, 21 Jun 2020 16:59:08: 3000000 INFO @ Sun, 21 Jun 2020 16:59:13: 4000000 INFO @ Sun, 21 Jun 2020 16:59:19: 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 16:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.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 16:59:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:59:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:59:24: 6000000 INFO @ Sun, 21 Jun 2020 16:59:27: 1000000 INFO @ Sun, 21 Jun 2020 16:59:30: 7000000 INFO @ Sun, 21 Jun 2020 16:59:32: 2000000 INFO @ Sun, 21 Jun 2020 16:59:34: #1 tag size is determined as 39 bps INFO @ Sun, 21 Jun 2020 16:59:34: #1 tag size = 39 INFO @ Sun, 21 Jun 2020 16:59:34: #1 total tags in treatment: 7764739 INFO @ Sun, 21 Jun 2020 16:59:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:59:34: #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 16:59:34: #1 tags after filtering in treatment: 7764633 INFO @ Sun, 21 Jun 2020 16:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:59:34: #1 finished! INFO @ Sun, 21 Jun 2020 16:59:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:59:35: #2 number of paired peaks: 1084 INFO @ Sun, 21 Jun 2020 16:59:35: start model_add_line... INFO @ Sun, 21 Jun 2020 16:59:35: start X-correlation... INFO @ Sun, 21 Jun 2020 16:59:35: end of X-cor INFO @ Sun, 21 Jun 2020 16:59:35: #2 finished! INFO @ Sun, 21 Jun 2020 16:59:35: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 16:59:35: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 16:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.05_model.r INFO @ Sun, 21 Jun 2020 16:59:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:59:37: 3000000 INFO @ Sun, 21 Jun 2020 16:59:42: 4000000 INFO @ Sun, 21 Jun 2020 16:59:47: 5000000 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 16:59:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.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 16:59:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:59:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:59:52: 6000000 INFO @ Sun, 21 Jun 2020 16:59:57: 1000000 INFO @ Sun, 21 Jun 2020 16:59:57: 7000000 INFO @ Sun, 21 Jun 2020 17:00:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.05_summits.bed INFO @ Sun, 21 Jun 2020 17:00:00: Done! pass1 - making usageList (511 chroms): 1 millis pass2 - checking and writing primary data (2140 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:00:02: #1 tag size is determined as 39 bps INFO @ Sun, 21 Jun 2020 17:00:02: #1 tag size = 39 INFO @ Sun, 21 Jun 2020 17:00:02: #1 total tags in treatment: 7764739 INFO @ Sun, 21 Jun 2020 17:00:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:02: #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 17:00:02: #1 tags after filtering in treatment: 7764633 INFO @ Sun, 21 Jun 2020 17:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:02: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:02: 2000000 INFO @ Sun, 21 Jun 2020 17:00:03: #2 number of paired peaks: 1084 INFO @ Sun, 21 Jun 2020 17:00:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:03: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 17:00:03: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 17:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.10_model.r INFO @ Sun, 21 Jun 2020 17:00:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:07: 3000000 INFO @ Sun, 21 Jun 2020 17:00:12: 4000000 INFO @ Sun, 21 Jun 2020 17:00:17: 5000000 INFO @ Sun, 21 Jun 2020 17:00:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:00:27: 7000000 INFO @ Sun, 21 Jun 2020 17:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.10_summits.bed INFO @ Sun, 21 Jun 2020 17:00:28: Done! pass1 - making usageList (251 chroms): 2 millis pass2 - checking and writing primary data (850 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:00:31: #1 tag size is determined as 39 bps INFO @ Sun, 21 Jun 2020 17:00:31: #1 tag size = 39 INFO @ Sun, 21 Jun 2020 17:00:31: #1 total tags in treatment: 7764739 INFO @ Sun, 21 Jun 2020 17:00:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:31: #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 17:00:32: #1 tags after filtering in treatment: 7764633 INFO @ Sun, 21 Jun 2020 17:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:32: #2 number of paired peaks: 1084 INFO @ Sun, 21 Jun 2020 17:00:32: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:32: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:32: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:32: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:32: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 17:00:32: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 17:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.20_model.r INFO @ Sun, 21 Jun 2020 17:00:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:00:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX018632/SRX018632.20_summits.bed INFO @ Sun, 21 Jun 2020 17:00:58: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (383 records, 4 fields): 4 millis CompletedMACS2peakCalling