Job ID = 6366063 SRX = SRX059235 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:27:29 prefetch.2.10.7: 1) Downloading 'SRR190675'... 2020-06-15T22:27:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:28:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:28:35 prefetch.2.10.7: 'SRR190675' is valid 2020-06-15T22:28:35 prefetch.2.10.7: 1) 'SRR190675' was downloaded successfully Read 15514273 spots for SRR190675/SRR190675.sra Written 15514273 spots for SRR190675/SRR190675.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: 00:02:40 15514273 reads; of these: 15514273 (100.00%) were unpaired; of these: 1189704 (7.67%) aligned 0 times 11745607 (75.71%) aligned exactly 1 time 2578962 (16.62%) aligned >1 times 92.33% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2909638 / 14324569 = 0.2031 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 @ Tue, 16 Jun 2020 07:35:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:35:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:35: 1000000 INFO @ Tue, 16 Jun 2020 07:35:41: 2000000 INFO @ Tue, 16 Jun 2020 07:35:47: 3000000 INFO @ Tue, 16 Jun 2020 07:35:53: 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 @ Tue, 16 Jun 2020 07:35:59: 5000000 INFO @ Tue, 16 Jun 2020 07:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:36:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:05: 6000000 INFO @ Tue, 16 Jun 2020 07:36:05: 1000000 INFO @ Tue, 16 Jun 2020 07:36:11: 2000000 INFO @ Tue, 16 Jun 2020 07:36:11: 7000000 INFO @ Tue, 16 Jun 2020 07:36:17: 3000000 INFO @ Tue, 16 Jun 2020 07:36:17: 8000000 INFO @ Tue, 16 Jun 2020 07:36:22: 4000000 INFO @ Tue, 16 Jun 2020 07:36:23: 9000000 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 @ Tue, 16 Jun 2020 07:36:28: 5000000 INFO @ Tue, 16 Jun 2020 07:36:29: 10000000 INFO @ Tue, 16 Jun 2020 07:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:36:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:34: 6000000 INFO @ Tue, 16 Jun 2020 07:36:35: 11000000 INFO @ Tue, 16 Jun 2020 07:36:36: 1000000 INFO @ Tue, 16 Jun 2020 07:36:38: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:36:38: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:36:38: #1 total tags in treatment: 11414931 INFO @ Tue, 16 Jun 2020 07:36:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:36:38: #1 tags after filtering in treatment: 11414931 INFO @ Tue, 16 Jun 2020 07:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:38: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:39: 7000000 INFO @ Tue, 16 Jun 2020 07:36:39: #2 number of paired peaks: 1441 INFO @ Tue, 16 Jun 2020 07:36:39: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:39: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:39: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:39: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:39: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 07:36:39: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 16 Jun 2020 07:36:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.05_model.r INFO @ Tue, 16 Jun 2020 07:36:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:41: 2000000 INFO @ Tue, 16 Jun 2020 07:36:45: 8000000 INFO @ Tue, 16 Jun 2020 07:36:47: 3000000 INFO @ Tue, 16 Jun 2020 07:36:50: 9000000 INFO @ Tue, 16 Jun 2020 07:36:53: 4000000 INFO @ Tue, 16 Jun 2020 07:36:56: 10000000 INFO @ Tue, 16 Jun 2020 07:36:59: 5000000 INFO @ Tue, 16 Jun 2020 07:37:02: 11000000 INFO @ Tue, 16 Jun 2020 07:37:04: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:37:04: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:37:04: #1 total tags in treatment: 11414931 INFO @ Tue, 16 Jun 2020 07:37:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:37:04: #1 tags after filtering in treatment: 11414931 INFO @ Tue, 16 Jun 2020 07:37:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:04: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:05: 6000000 INFO @ Tue, 16 Jun 2020 07:37:05: #2 number of paired peaks: 1441 INFO @ Tue, 16 Jun 2020 07:37:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:05: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 07:37:05: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 16 Jun 2020 07:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.10_model.r INFO @ Tue, 16 Jun 2020 07:37:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:11: 7000000 INFO @ Tue, 16 Jun 2020 07:37:16: 8000000 INFO @ Tue, 16 Jun 2020 07:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.05_summits.bed INFO @ Tue, 16 Jun 2020 07:37:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4391 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:37:22: 9000000 INFO @ Tue, 16 Jun 2020 07:37:28: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:37:33: 11000000 INFO @ Tue, 16 Jun 2020 07:37:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:36: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:37:36: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:37:36: #1 total tags in treatment: 11414931 INFO @ Tue, 16 Jun 2020 07:37:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:37:36: #1 tags after filtering in treatment: 11414931 INFO @ Tue, 16 Jun 2020 07:37:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:37: #2 number of paired peaks: 1441 INFO @ Tue, 16 Jun 2020 07:37:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:37: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 07:37:37: #2 alternative fragment length(s) may be 101 bps INFO @ Tue, 16 Jun 2020 07:37:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.20_model.r INFO @ Tue, 16 Jun 2020 07:37:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.10_summits.bed INFO @ Tue, 16 Jun 2020 07:37:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2841 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:38:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:38:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:38:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:38:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059235/SRX059235.20_summits.bed INFO @ Tue, 16 Jun 2020 07:38:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1778 records, 4 fields): 5 millis CompletedMACS2peakCalling