Job ID = 6368305 SRX = SRX494988 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:02:30 prefetch.2.10.7: 1) Downloading 'SRR1198520'... 2020-06-16T00:02:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:02:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:02:58 prefetch.2.10.7: 'SRR1198520' is valid 2020-06-16T00:02:58 prefetch.2.10.7: 1) 'SRR1198520' was downloaded successfully Read 4716670 spots for SRR1198520/SRR1198520.sra Written 4716670 spots for SRR1198520/SRR1198520.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: 00:00:52 4716670 reads; of these: 4716670 (100.00%) were unpaired; of these: 127083 (2.69%) aligned 0 times 3941675 (83.57%) aligned exactly 1 time 647912 (13.74%) aligned >1 times 97.31% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 1238666 / 4589587 = 0.2699 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 09:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.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 09:05:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:33: 1000000 INFO @ Tue, 16 Jun 2020 09:05:39: 2000000 INFO @ Tue, 16 Jun 2020 09:05:45: 3000000 INFO @ Tue, 16 Jun 2020 09:05:47: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:05:47: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:05:47: #1 total tags in treatment: 3350921 INFO @ Tue, 16 Jun 2020 09:05:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:47: #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 09:05:47: #1 tags after filtering in treatment: 3350921 INFO @ Tue, 16 Jun 2020 09:05:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:47: #2 number of paired peaks: 2755 INFO @ Tue, 16 Jun 2020 09:05:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:47: #2 predicted fragment length is 228 bps INFO @ Tue, 16 Jun 2020 09:05:47: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 16 Jun 2020 09:05:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.05_model.r INFO @ Tue, 16 Jun 2020 09:05:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:47: #3 Pre-compute pvalue-qvalue table... 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 09:05:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.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 09:05:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.05_summits.bed INFO @ Tue, 16 Jun 2020 09:06:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5438 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:03: 1000000 INFO @ Tue, 16 Jun 2020 09:06:08: 2000000 INFO @ Tue, 16 Jun 2020 09:06:14: 3000000 INFO @ Tue, 16 Jun 2020 09:06:16: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:06:16: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:06:16: #1 total tags in treatment: 3350921 INFO @ Tue, 16 Jun 2020 09:06:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:16: #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 09:06:16: #1 tags after filtering in treatment: 3350921 INFO @ Tue, 16 Jun 2020 09:06:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:16: #2 number of paired peaks: 2755 INFO @ Tue, 16 Jun 2020 09:06:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:17: #2 predicted fragment length is 228 bps INFO @ Tue, 16 Jun 2020 09:06:17: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 16 Jun 2020 09:06:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.10_model.r INFO @ Tue, 16 Jun 2020 09:06:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:17: #3 Pre-compute pvalue-qvalue table... 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 09:06:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.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 09:06:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.10_summits.bed INFO @ Tue, 16 Jun 2020 09:06:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3208 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:33: 1000000 INFO @ Tue, 16 Jun 2020 09:06:39: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:06:45: 3000000 INFO @ Tue, 16 Jun 2020 09:06:47: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:06:47: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:06:47: #1 total tags in treatment: 3350921 INFO @ Tue, 16 Jun 2020 09:06:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:47: #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 09:06:47: #1 tags after filtering in treatment: 3350921 INFO @ Tue, 16 Jun 2020 09:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:48: #2 number of paired peaks: 2755 INFO @ Tue, 16 Jun 2020 09:06:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:48: #2 predicted fragment length is 228 bps INFO @ Tue, 16 Jun 2020 09:06:48: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 16 Jun 2020 09:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.20_model.r INFO @ Tue, 16 Jun 2020 09:06:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:06:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494988/SRX494988.20_summits.bed INFO @ Tue, 16 Jun 2020 09:07:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1871 records, 4 fields): 3 millis CompletedMACS2peakCalling