Job ID = 6457488 SRX = SRX4664646 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:53:51 prefetch.2.10.7: 1) Downloading 'SRR7813073'... 2020-06-21T11:53:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:56:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:56:49 prefetch.2.10.7: 'SRR7813073' is valid 2020-06-21T11:56:49 prefetch.2.10.7: 1) 'SRR7813073' was downloaded successfully Read 18255858 spots for SRR7813073/SRR7813073.sra Written 18255858 spots for SRR7813073/SRR7813073.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: 00:05:00 18255858 reads; of these: 18255858 (100.00%) were unpaired; of these: 577058 (3.16%) aligned 0 times 13162527 (72.10%) aligned exactly 1 time 4516273 (24.74%) aligned >1 times 96.84% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 4628245 / 17678800 = 0.2618 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 21:06:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.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 21:06:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:06:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:06:27: 1000000 INFO @ Sun, 21 Jun 2020 21:06:32: 2000000 INFO @ Sun, 21 Jun 2020 21:06:37: 3000000 INFO @ Sun, 21 Jun 2020 21:06:42: 4000000 INFO @ Sun, 21 Jun 2020 21:06:47: 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 21:06:52: 6000000 INFO @ Sun, 21 Jun 2020 21:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.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 21:06:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:06:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:06:57: 7000000 INFO @ Sun, 21 Jun 2020 21:06:58: 1000000 INFO @ Sun, 21 Jun 2020 21:07:02: 8000000 INFO @ Sun, 21 Jun 2020 21:07:03: 2000000 INFO @ Sun, 21 Jun 2020 21:07:07: 9000000 INFO @ Sun, 21 Jun 2020 21:07:08: 3000000 INFO @ Sun, 21 Jun 2020 21:07:12: 10000000 INFO @ Sun, 21 Jun 2020 21:07:13: 4000000 INFO @ Sun, 21 Jun 2020 21:07:18: 11000000 INFO @ Sun, 21 Jun 2020 21:07:18: 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 21:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.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 21:07:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:23: 12000000 INFO @ Sun, 21 Jun 2020 21:07:23: 6000000 INFO @ Sun, 21 Jun 2020 21:07:28: 13000000 INFO @ Sun, 21 Jun 2020 21:07:29: 7000000 INFO @ Sun, 21 Jun 2020 21:07:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:07:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:07:29: #1 total tags in treatment: 13050555 INFO @ Sun, 21 Jun 2020 21:07:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:07:29: #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 21:07:29: 1000000 INFO @ Sun, 21 Jun 2020 21:07:29: #1 tags after filtering in treatment: 13050460 INFO @ Sun, 21 Jun 2020 21:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:07:29: #1 finished! INFO @ Sun, 21 Jun 2020 21:07:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:07:30: #2 number of paired peaks: 3433 INFO @ Sun, 21 Jun 2020 21:07:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:07:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:07:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:07:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:07:31: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:07:31: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.05_model.r INFO @ Sun, 21 Jun 2020 21:07:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:07:34: 8000000 INFO @ Sun, 21 Jun 2020 21:07:35: 2000000 INFO @ Sun, 21 Jun 2020 21:07:40: 9000000 INFO @ Sun, 21 Jun 2020 21:07:42: 3000000 INFO @ Sun, 21 Jun 2020 21:07:45: 10000000 INFO @ Sun, 21 Jun 2020 21:07:48: 4000000 INFO @ Sun, 21 Jun 2020 21:07:51: 11000000 INFO @ Sun, 21 Jun 2020 21:07:54: 5000000 INFO @ Sun, 21 Jun 2020 21:07:56: 12000000 INFO @ Sun, 21 Jun 2020 21:08:00: 6000000 INFO @ Sun, 21 Jun 2020 21:08:02: 13000000 INFO @ Sun, 21 Jun 2020 21:08:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:08:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:08:02: #1 total tags in treatment: 13050555 INFO @ Sun, 21 Jun 2020 21:08:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:08:02: #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 21:08:03: #1 tags after filtering in treatment: 13050460 INFO @ Sun, 21 Jun 2020 21:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:08:03: #1 finished! INFO @ Sun, 21 Jun 2020 21:08:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:08:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:04: #2 number of paired peaks: 3433 INFO @ Sun, 21 Jun 2020 21:08:04: start model_add_line... INFO @ Sun, 21 Jun 2020 21:08:04: start X-correlation... INFO @ Sun, 21 Jun 2020 21:08:04: end of X-cor INFO @ Sun, 21 Jun 2020 21:08:04: #2 finished! INFO @ Sun, 21 Jun 2020 21:08:04: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:08:04: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.10_model.r INFO @ Sun, 21 Jun 2020 21:08:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:08:06: 7000000 INFO @ Sun, 21 Jun 2020 21:08:12: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:08:18: 9000000 INFO @ Sun, 21 Jun 2020 21:08:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:08:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:08:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.05_summits.bed INFO @ Sun, 21 Jun 2020 21:08:20: Done! pass1 - making usageList (576 chroms): 2 millis pass2 - checking and writing primary data (11531 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:08:24: 10000000 INFO @ Sun, 21 Jun 2020 21:08:30: 11000000 INFO @ Sun, 21 Jun 2020 21:08:36: 12000000 INFO @ Sun, 21 Jun 2020 21:08:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:42: 13000000 INFO @ Sun, 21 Jun 2020 21:08:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:08:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:08:43: #1 total tags in treatment: 13050555 INFO @ Sun, 21 Jun 2020 21:08:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:08:43: #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 21:08:43: #1 tags after filtering in treatment: 13050460 INFO @ Sun, 21 Jun 2020 21:08:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:08:43: #1 finished! INFO @ Sun, 21 Jun 2020 21:08:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:08:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:08:44: #2 number of paired peaks: 3433 INFO @ Sun, 21 Jun 2020 21:08:44: start model_add_line... INFO @ Sun, 21 Jun 2020 21:08:44: start X-correlation... INFO @ Sun, 21 Jun 2020 21:08:44: end of X-cor INFO @ Sun, 21 Jun 2020 21:08:44: #2 finished! INFO @ Sun, 21 Jun 2020 21:08:44: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:08:44: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:08:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.20_model.r INFO @ Sun, 21 Jun 2020 21:08:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:08:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.10_summits.bed INFO @ Sun, 21 Jun 2020 21:08:54: Done! pass1 - making usageList (499 chroms): 2 millis pass2 - checking and writing primary data (9027 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:09:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664646/SRX4664646.20_summits.bed INFO @ Sun, 21 Jun 2020 21:09:35: Done! pass1 - making usageList (373 chroms): 1 millis pass2 - checking and writing primary data (6109 records, 4 fields): 37 millis CompletedMACS2peakCalling