Job ID = 6457942 SRX = SRX4923186 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:02:38 prefetch.2.10.7: 1) Downloading 'SRR8096336'... 2020-06-21T12:02:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:04:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:04:01 prefetch.2.10.7: 'SRR8096336' is valid 2020-06-21T12:04:01 prefetch.2.10.7: 1) 'SRR8096336' was downloaded successfully 2020-06-21T12:04:01 prefetch.2.10.7: 'SRR8096336' has 0 unresolved dependencies Read 17317193 spots for SRR8096336/SRR8096336.sra Written 17317193 spots for SRR8096336/SRR8096336.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: 00:03:55 17317193 reads; of these: 17317193 (100.00%) were unpaired; of these: 414441 (2.39%) aligned 0 times 13711214 (79.18%) aligned exactly 1 time 3191538 (18.43%) aligned >1 times 97.61% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 5303295 / 16902752 = 0.3138 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 21:11:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.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 21:11:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:04: 1000000 INFO @ Sun, 21 Jun 2020 21:12:09: 2000000 INFO @ Sun, 21 Jun 2020 21:12:14: 3000000 INFO @ Sun, 21 Jun 2020 21:12:19: 4000000 INFO @ Sun, 21 Jun 2020 21:12:24: 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 21:12:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.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 21:12:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:12:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:29: 6000000 INFO @ Sun, 21 Jun 2020 21:12:35: 1000000 INFO @ Sun, 21 Jun 2020 21:12:35: 7000000 INFO @ Sun, 21 Jun 2020 21:12:41: 2000000 INFO @ Sun, 21 Jun 2020 21:12:41: 8000000 INFO @ Sun, 21 Jun 2020 21:12:46: 3000000 INFO @ Sun, 21 Jun 2020 21:12:47: 9000000 INFO @ Sun, 21 Jun 2020 21:12:52: 4000000 INFO @ Sun, 21 Jun 2020 21:12:53: 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 21:12:58: 5000000 INFO @ Sun, 21 Jun 2020 21:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.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 21:12:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:12:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:59: 11000000 INFO @ Sun, 21 Jun 2020 21:13:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:13:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:13:02: #1 total tags in treatment: 11599457 INFO @ Sun, 21 Jun 2020 21:13:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:02: #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 21:13:03: #1 tags after filtering in treatment: 11599328 INFO @ Sun, 21 Jun 2020 21:13:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:03: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:03: 6000000 INFO @ Sun, 21 Jun 2020 21:13:04: #2 number of paired peaks: 8959 INFO @ Sun, 21 Jun 2020 21:13:04: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:04: 1000000 INFO @ Sun, 21 Jun 2020 21:13:04: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:04: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:04: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:04: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 21:13:04: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 21:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.05_model.r INFO @ Sun, 21 Jun 2020 21:13:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:13:09: 7000000 INFO @ Sun, 21 Jun 2020 21:13:10: 2000000 INFO @ Sun, 21 Jun 2020 21:13:15: 8000000 INFO @ Sun, 21 Jun 2020 21:13:16: 3000000 INFO @ Sun, 21 Jun 2020 21:13:20: 9000000 INFO @ Sun, 21 Jun 2020 21:13:21: 4000000 INFO @ Sun, 21 Jun 2020 21:13:26: 10000000 INFO @ Sun, 21 Jun 2020 21:13:27: 5000000 INFO @ Sun, 21 Jun 2020 21:13:32: 11000000 INFO @ Sun, 21 Jun 2020 21:13:32: 6000000 INFO @ Sun, 21 Jun 2020 21:13:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:13:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:13:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:13:36: #1 total tags in treatment: 11599457 INFO @ Sun, 21 Jun 2020 21:13:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:36: #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 21:13:36: #1 tags after filtering in treatment: 11599328 INFO @ Sun, 21 Jun 2020 21:13:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:38: #2 number of paired peaks: 8959 INFO @ Sun, 21 Jun 2020 21:13:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:38: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 21:13:38: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 21:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.10_model.r INFO @ Sun, 21 Jun 2020 21:13:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:13:38: 7000000 INFO @ Sun, 21 Jun 2020 21:13:43: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.05_summits.bed INFO @ Sun, 21 Jun 2020 21:13:46: Done! pass1 - making usageList (575 chroms): 2 millis pass2 - checking and writing primary data (9719 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:13:49: 9000000 INFO @ Sun, 21 Jun 2020 21:13:54: 10000000 INFO @ Sun, 21 Jun 2020 21:13:59: 11000000 INFO @ Sun, 21 Jun 2020 21:14:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:14:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:14:03: #1 total tags in treatment: 11599457 INFO @ Sun, 21 Jun 2020 21:14:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:03: #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 21:14:03: #1 tags after filtering in treatment: 11599328 INFO @ Sun, 21 Jun 2020 21:14:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:14:03: #1 finished! INFO @ Sun, 21 Jun 2020 21:14:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:14:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:14:05: #2 number of paired peaks: 8959 INFO @ Sun, 21 Jun 2020 21:14:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:14:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:14:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:14:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:14:05: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 21:14:05: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 21:14:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.20_model.r INFO @ Sun, 21 Jun 2020 21:14:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:14:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:14:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:14:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.10_summits.bed INFO @ Sun, 21 Jun 2020 21:14:21: Done! pass1 - making usageList (482 chroms): 2 millis pass2 - checking and writing primary data (8573 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:14:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923186/SRX4923186.20_summits.bed INFO @ Sun, 21 Jun 2020 21:14:50: Done! pass1 - making usageList (283 chroms): 1 millis pass2 - checking and writing primary data (6673 records, 4 fields): 19 millis CompletedMACS2peakCalling