Job ID = 6368302 SRX = SRX494985 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:15 prefetch.2.10.7: 1) Downloading 'SRR1198517'... 2020-06-16T00:04:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:48 prefetch.2.10.7: 'SRR1198517' is valid 2020-06-16T00:05:48 prefetch.2.10.7: 1) 'SRR1198517' was downloaded successfully Read 11592817 spots for SRR1198517/SRR1198517.sra Written 11592817 spots for SRR1198517/SRR1198517.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: 00:02:28 11592817 reads; of these: 11592817 (100.00%) were unpaired; of these: 535821 (4.62%) aligned 0 times 8961077 (77.30%) aligned exactly 1 time 2095919 (18.08%) aligned >1 times 95.38% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 2180629 / 11056996 = 0.1972 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 09:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.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 09:11:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:35: 1000000 INFO @ Tue, 16 Jun 2020 09:11:41: 2000000 INFO @ Tue, 16 Jun 2020 09:11:47: 3000000 INFO @ Tue, 16 Jun 2020 09:11:53: 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 09:11:58: 5000000 INFO @ Tue, 16 Jun 2020 09:12:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.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 09:12:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:05: 6000000 INFO @ Tue, 16 Jun 2020 09:12:06: 1000000 INFO @ Tue, 16 Jun 2020 09:12:11: 7000000 INFO @ Tue, 16 Jun 2020 09:12:13: 2000000 INFO @ Tue, 16 Jun 2020 09:12:18: 8000000 INFO @ Tue, 16 Jun 2020 09:12:19: 3000000 INFO @ Tue, 16 Jun 2020 09:12:24: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:24: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:24: #1 total tags in treatment: 8876367 INFO @ Tue, 16 Jun 2020 09:12:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:24: #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 09:12:24: #1 tags after filtering in treatment: 8876367 INFO @ Tue, 16 Jun 2020 09:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:24: #2 number of paired peaks: 1129 INFO @ Tue, 16 Jun 2020 09:12:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:24: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 09:12:24: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 09:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.05_model.r INFO @ Tue, 16 Jun 2020 09:12:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:25: 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 09:12:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.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 09:12:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:31: 5000000 INFO @ Tue, 16 Jun 2020 09:12:36: 1000000 INFO @ Tue, 16 Jun 2020 09:12:38: 6000000 INFO @ Tue, 16 Jun 2020 09:12:43: 2000000 INFO @ Tue, 16 Jun 2020 09:12:44: 7000000 INFO @ Tue, 16 Jun 2020 09:12:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:49: 3000000 INFO @ Tue, 16 Jun 2020 09:12:51: 8000000 INFO @ Tue, 16 Jun 2020 09:12:56: 4000000 INFO @ Tue, 16 Jun 2020 09:12:56: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:56: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:56: #1 total tags in treatment: 8876367 INFO @ Tue, 16 Jun 2020 09:12:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:56: #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 09:12:57: #1 tags after filtering in treatment: 8876367 INFO @ Tue, 16 Jun 2020 09:12:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:57: #2 number of paired peaks: 1129 INFO @ Tue, 16 Jun 2020 09:12:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:57: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 09:12:57: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 09:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.10_model.r INFO @ Tue, 16 Jun 2020 09:12:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:58: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6975 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:02: 5000000 INFO @ Tue, 16 Jun 2020 09:13:08: 6000000 INFO @ Tue, 16 Jun 2020 09:13:14: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:20: 8000000 INFO @ Tue, 16 Jun 2020 09:13:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:26: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:26: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:26: #1 total tags in treatment: 8876367 INFO @ Tue, 16 Jun 2020 09:13:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:26: #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 09:13:26: #1 tags after filtering in treatment: 8876367 INFO @ Tue, 16 Jun 2020 09:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:26: #2 number of paired peaks: 1129 INFO @ Tue, 16 Jun 2020 09:13:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:27: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 09:13:27: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 16 Jun 2020 09:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.20_model.r INFO @ Tue, 16 Jun 2020 09:13:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3045 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494985/SRX494985.20_summits.bed INFO @ Tue, 16 Jun 2020 09:14:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1002 records, 4 fields): 2 millis CompletedMACS2peakCalling