Job ID = 6366495 SRX = SRX148637 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:47:56 prefetch.2.10.7: 1) Downloading 'SRR498190'... 2020-06-15T22:47:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:48:48 prefetch.2.10.7: 'SRR498190' is valid 2020-06-15T22:48:48 prefetch.2.10.7: 1) 'SRR498190' was downloaded successfully Read 15301248 spots for SRR498190/SRR498190.sra Written 15301248 spots for SRR498190/SRR498190.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: 00:03:24 15301248 reads; of these: 15301248 (100.00%) were unpaired; of these: 851321 (5.56%) aligned 0 times 9700618 (63.40%) aligned exactly 1 time 4749309 (31.04%) aligned >1 times 94.44% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 7666855 / 14449927 = 0.5306 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 07:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.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 07:55:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:56: 1000000 INFO @ Tue, 16 Jun 2020 07:56:03: 2000000 INFO @ Tue, 16 Jun 2020 07:56:09: 3000000 INFO @ Tue, 16 Jun 2020 07:56:16: 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 07:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.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 07:56:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:23: 5000000 INFO @ Tue, 16 Jun 2020 07:56:27: 1000000 INFO @ Tue, 16 Jun 2020 07:56:30: 6000000 INFO @ Tue, 16 Jun 2020 07:56:34: 2000000 INFO @ Tue, 16 Jun 2020 07:56:36: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:56:36: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:56:36: #1 total tags in treatment: 6783072 INFO @ Tue, 16 Jun 2020 07:56:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:36: #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 07:56:36: #1 tags after filtering in treatment: 6783072 INFO @ Tue, 16 Jun 2020 07:56:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:36: #2 number of paired peaks: 5279 INFO @ Tue, 16 Jun 2020 07:56:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:37: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 07:56:37: #2 alternative fragment length(s) may be 1,141 bps INFO @ Tue, 16 Jun 2020 07:56:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.05_model.r INFO @ Tue, 16 Jun 2020 07:56:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:56:41: 3000000 INFO @ Tue, 16 Jun 2020 07:56:47: 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 @ Tue, 16 Jun 2020 07:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.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 07:56:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:56:53: 5000000 INFO @ Tue, 16 Jun 2020 07:56:56: 1000000 INFO @ Tue, 16 Jun 2020 07:57:00: 6000000 INFO @ Tue, 16 Jun 2020 07:57:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.05_summits.bed INFO @ Tue, 16 Jun 2020 07:57:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (3662 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:57:03: 2000000 INFO @ Tue, 16 Jun 2020 07:57:04: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:57:04: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:57:04: #1 total tags in treatment: 6783072 INFO @ Tue, 16 Jun 2020 07:57:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:04: #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 07:57:05: #1 tags after filtering in treatment: 6783072 INFO @ Tue, 16 Jun 2020 07:57:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:05: #2 number of paired peaks: 5279 INFO @ Tue, 16 Jun 2020 07:57:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:06: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 07:57:06: #2 alternative fragment length(s) may be 1,141 bps INFO @ Tue, 16 Jun 2020 07:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.10_model.r INFO @ Tue, 16 Jun 2020 07:57:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:57:09: 3000000 INFO @ Tue, 16 Jun 2020 07:57:15: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:57:21: 5000000 INFO @ Tue, 16 Jun 2020 07:57:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:27: 6000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:57:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.10_summits.bed INFO @ Tue, 16 Jun 2020 07:57:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1098 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:57:32: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:57:32: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:57:32: #1 total tags in treatment: 6783072 INFO @ Tue, 16 Jun 2020 07:57:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:32: #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 07:57:32: #1 tags after filtering in treatment: 6783072 INFO @ Tue, 16 Jun 2020 07:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:32: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:33: #2 number of paired peaks: 5279 INFO @ Tue, 16 Jun 2020 07:57:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:33: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 07:57:33: #2 alternative fragment length(s) may be 1,141 bps INFO @ Tue, 16 Jun 2020 07:57:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.20_model.r INFO @ Tue, 16 Jun 2020 07:57:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:57:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX148637/SRX148637.20_summits.bed INFO @ Tue, 16 Jun 2020 07:57:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (255 records, 4 fields): 1 millis CompletedMACS2peakCalling