Job ID = 6508509 SRX = SRX297097 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:21:43 prefetch.2.10.7: 1) Downloading 'SRR886298'... 2020-06-26T14:21:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:24:14 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:24:14 prefetch.2.10.7: 1) 'SRR886298' was downloaded successfully Read 28354404 spots for SRR886298/SRR886298.sra Written 28354404 spots for SRR886298/SRR886298.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: 00:10:20 28354404 reads; of these: 28354404 (100.00%) were unpaired; of these: 1866656 (6.58%) aligned 0 times 16511799 (58.23%) aligned exactly 1 time 9975949 (35.18%) aligned >1 times 93.42% overall alignment rate Time searching: 00:10:20 Overall time: 00:10:20 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 12 files... [bam_rmdupse_core] 15604026 / 26487748 = 0.5891 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 @ Fri, 26 Jun 2020 23:41:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.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 @ Fri, 26 Jun 2020 23:41:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:41:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:41:53: 1000000 INFO @ Fri, 26 Jun 2020 23:41:59: 2000000 INFO @ Fri, 26 Jun 2020 23:42:05: 3000000 INFO @ Fri, 26 Jun 2020 23:42:11: 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 @ Fri, 26 Jun 2020 23:42:17: 5000000 INFO @ Fri, 26 Jun 2020 23:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.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 @ Fri, 26 Jun 2020 23:42:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:42:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:42:23: 6000000 INFO @ Fri, 26 Jun 2020 23:42:23: 1000000 INFO @ Fri, 26 Jun 2020 23:42:30: 7000000 INFO @ Fri, 26 Jun 2020 23:42:30: 2000000 INFO @ Fri, 26 Jun 2020 23:42:36: 8000000 INFO @ Fri, 26 Jun 2020 23:42:37: 3000000 INFO @ Fri, 26 Jun 2020 23:42:43: 9000000 INFO @ Fri, 26 Jun 2020 23:42:43: 4000000 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 @ Fri, 26 Jun 2020 23:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.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 @ Fri, 26 Jun 2020 23:42:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:42:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:42:50: 10000000 INFO @ Fri, 26 Jun 2020 23:42:50: 5000000 INFO @ Fri, 26 Jun 2020 23:42:53: 1000000 INFO @ Fri, 26 Jun 2020 23:42:56: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:42:56: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:42:56: #1 total tags in treatment: 10883722 INFO @ Fri, 26 Jun 2020 23:42:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:42:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:42:56: #1 tags after filtering in treatment: 10883594 INFO @ Fri, 26 Jun 2020 23:42:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:42:56: #1 finished! INFO @ Fri, 26 Jun 2020 23:42:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:42:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:42:56: 6000000 INFO @ Fri, 26 Jun 2020 23:42:57: #2 number of paired peaks: 6297 INFO @ Fri, 26 Jun 2020 23:42:57: start model_add_line... INFO @ Fri, 26 Jun 2020 23:42:58: start X-correlation... INFO @ Fri, 26 Jun 2020 23:42:58: end of X-cor INFO @ Fri, 26 Jun 2020 23:42:58: #2 finished! INFO @ Fri, 26 Jun 2020 23:42:58: #2 predicted fragment length is 122 bps INFO @ Fri, 26 Jun 2020 23:42:58: #2 alternative fragment length(s) may be 4,122 bps INFO @ Fri, 26 Jun 2020 23:42:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.05_model.r INFO @ Fri, 26 Jun 2020 23:42:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:43:00: 2000000 INFO @ Fri, 26 Jun 2020 23:43:03: 7000000 INFO @ Fri, 26 Jun 2020 23:43:07: 3000000 INFO @ Fri, 26 Jun 2020 23:43:10: 8000000 INFO @ Fri, 26 Jun 2020 23:43:13: 4000000 INFO @ Fri, 26 Jun 2020 23:43:17: 9000000 INFO @ Fri, 26 Jun 2020 23:43:20: 5000000 INFO @ Fri, 26 Jun 2020 23:43:23: 10000000 INFO @ Fri, 26 Jun 2020 23:43:27: 6000000 INFO @ Fri, 26 Jun 2020 23:43:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:43:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:43:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:43:29: #1 total tags in treatment: 10883722 INFO @ Fri, 26 Jun 2020 23:43:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:43:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:43:30: #1 tags after filtering in treatment: 10883594 INFO @ Fri, 26 Jun 2020 23:43:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:43:30: #1 finished! INFO @ Fri, 26 Jun 2020 23:43:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:43:31: #2 number of paired peaks: 6297 INFO @ Fri, 26 Jun 2020 23:43:31: start model_add_line... INFO @ Fri, 26 Jun 2020 23:43:31: start X-correlation... INFO @ Fri, 26 Jun 2020 23:43:31: end of X-cor INFO @ Fri, 26 Jun 2020 23:43:31: #2 finished! INFO @ Fri, 26 Jun 2020 23:43:31: #2 predicted fragment length is 122 bps INFO @ Fri, 26 Jun 2020 23:43:31: #2 alternative fragment length(s) may be 4,122 bps INFO @ Fri, 26 Jun 2020 23:43:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.10_model.r INFO @ Fri, 26 Jun 2020 23:43:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:43:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:43:33: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:43:39: 8000000 INFO @ Fri, 26 Jun 2020 23:43:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:43:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:43:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.05_summits.bed INFO @ Fri, 26 Jun 2020 23:43:43: Done! pass1 - making usageList (592 chroms): 2 millis pass2 - checking and writing primary data (13079 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:43:45: 9000000 INFO @ Fri, 26 Jun 2020 23:43:51: 10000000 INFO @ Fri, 26 Jun 2020 23:43:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:43:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:43:57: #1 total tags in treatment: 10883722 INFO @ Fri, 26 Jun 2020 23:43:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:43:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:43:58: #1 tags after filtering in treatment: 10883594 INFO @ Fri, 26 Jun 2020 23:43:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:43:58: #1 finished! INFO @ Fri, 26 Jun 2020 23:43:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:43:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:43:59: #2 number of paired peaks: 6297 INFO @ Fri, 26 Jun 2020 23:43:59: start model_add_line... INFO @ Fri, 26 Jun 2020 23:43:59: start X-correlation... INFO @ Fri, 26 Jun 2020 23:43:59: end of X-cor INFO @ Fri, 26 Jun 2020 23:43:59: #2 finished! INFO @ Fri, 26 Jun 2020 23:43:59: #2 predicted fragment length is 122 bps INFO @ Fri, 26 Jun 2020 23:43:59: #2 alternative fragment length(s) may be 4,122 bps INFO @ Fri, 26 Jun 2020 23:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.20_model.r INFO @ Fri, 26 Jun 2020 23:43:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:44:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:44:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:44:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:44:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.10_summits.bed INFO @ Fri, 26 Jun 2020 23:44:16: Done! pass1 - making usageList (417 chroms): 2 millis pass2 - checking and writing primary data (9893 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:44:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX297097/SRX297097.20_summits.bed INFO @ Fri, 26 Jun 2020 23:44:44: Done! pass1 - making usageList (245 chroms): 1 millis pass2 - checking and writing primary data (5223 records, 4 fields): 14 millis CompletedMACS2peakCalling