Job ID = 6497468 SRX = SRX494969 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:38:54 prefetch.2.10.7: 1) Downloading 'SRR1198501'... 2020-06-25T21:38:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:39:56 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:39:57 prefetch.2.10.7: 'SRR1198501' is valid 2020-06-25T21:39:57 prefetch.2.10.7: 1) 'SRR1198501' was downloaded successfully Read 8451937 spots for SRR1198501/SRR1198501.sra Written 8451937 spots for SRR1198501/SRR1198501.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: 00:01:41 8451937 reads; of these: 8451937 (100.00%) were unpaired; of these: 1136939 (13.45%) aligned 0 times 6209818 (73.47%) aligned exactly 1 time 1105180 (13.08%) aligned >1 times 86.55% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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] 4145223 / 7314998 = 0.5667 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 06:44:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.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 @ Fri, 26 Jun 2020 06:44:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:44:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:44:32: 1000000 INFO @ Fri, 26 Jun 2020 06:44:37: 2000000 INFO @ Fri, 26 Jun 2020 06:44:43: 3000000 INFO @ Fri, 26 Jun 2020 06:44:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:44:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:44:44: #1 total tags in treatment: 3169775 INFO @ Fri, 26 Jun 2020 06:44:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:44:44: #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 06:44:44: #1 tags after filtering in treatment: 3169775 INFO @ Fri, 26 Jun 2020 06:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:44:44: #1 finished! INFO @ Fri, 26 Jun 2020 06:44:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:44:44: #2 number of paired peaks: 2043 INFO @ Fri, 26 Jun 2020 06:44:44: start model_add_line... INFO @ Fri, 26 Jun 2020 06:44:44: start X-correlation... INFO @ Fri, 26 Jun 2020 06:44:44: end of X-cor INFO @ Fri, 26 Jun 2020 06:44:44: #2 finished! INFO @ Fri, 26 Jun 2020 06:44:44: #2 predicted fragment length is 120 bps INFO @ Fri, 26 Jun 2020 06:44:44: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 26 Jun 2020 06:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.05_model.r INFO @ Fri, 26 Jun 2020 06:44:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:44:51: #3 Call peaks for each chromosome... 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 06:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.05_summits.bed INFO @ Fri, 26 Jun 2020 06:44:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3337 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.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 @ Fri, 26 Jun 2020 06:44:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:44:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:45:02: 1000000 INFO @ Fri, 26 Jun 2020 06:45:07: 2000000 INFO @ Fri, 26 Jun 2020 06:45:13: 3000000 INFO @ Fri, 26 Jun 2020 06:45:14: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:45:14: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:45:14: #1 total tags in treatment: 3169775 INFO @ Fri, 26 Jun 2020 06:45:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:45:14: #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 06:45:14: #1 tags after filtering in treatment: 3169775 INFO @ Fri, 26 Jun 2020 06:45:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:45:14: #1 finished! INFO @ Fri, 26 Jun 2020 06:45:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:45:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:45:15: #2 number of paired peaks: 2043 INFO @ Fri, 26 Jun 2020 06:45:15: start model_add_line... INFO @ Fri, 26 Jun 2020 06:45:15: start X-correlation... INFO @ Fri, 26 Jun 2020 06:45:15: end of X-cor INFO @ Fri, 26 Jun 2020 06:45:15: #2 finished! INFO @ Fri, 26 Jun 2020 06:45:15: #2 predicted fragment length is 120 bps INFO @ Fri, 26 Jun 2020 06:45:15: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 26 Jun 2020 06:45:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.10_model.r INFO @ Fri, 26 Jun 2020 06:45:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:45:17: #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 @ Fri, 26 Jun 2020 06:45:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:45:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.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 @ Fri, 26 Jun 2020 06:45:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:45:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.10_summits.bed INFO @ Fri, 26 Jun 2020 06:45:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2455 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:45:32: 1000000 INFO @ Fri, 26 Jun 2020 06:45:38: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:45:43: 3000000 INFO @ Fri, 26 Jun 2020 06:45:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:45:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:45:44: #1 total tags in treatment: 3169775 INFO @ Fri, 26 Jun 2020 06:45:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:45:44: #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 06:45:44: #1 tags after filtering in treatment: 3169775 INFO @ Fri, 26 Jun 2020 06:45:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:45:44: #1 finished! INFO @ Fri, 26 Jun 2020 06:45:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:45:45: #2 number of paired peaks: 2043 INFO @ Fri, 26 Jun 2020 06:45:45: start model_add_line... INFO @ Fri, 26 Jun 2020 06:45:45: start X-correlation... INFO @ Fri, 26 Jun 2020 06:45:45: end of X-cor INFO @ Fri, 26 Jun 2020 06:45:45: #2 finished! INFO @ Fri, 26 Jun 2020 06:45:45: #2 predicted fragment length is 120 bps INFO @ Fri, 26 Jun 2020 06:45:45: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 26 Jun 2020 06:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.20_model.r INFO @ Fri, 26 Jun 2020 06:45:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:45:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494969/SRX494969.20_summits.bed INFO @ Fri, 26 Jun 2020 06:45:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1443 records, 4 fields): 4 millis CompletedMACS2peakCalling