Job ID = 6366061 SRX = SRX059233 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:50:41 prefetch.2.10.7: 1) Downloading 'SRR190673'... 2020-06-15T22:50:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:51:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:51:47 prefetch.2.10.7: 'SRR190673' is valid 2020-06-15T22:51:47 prefetch.2.10.7: 1) 'SRR190673' was downloaded successfully Read 15907024 spots for SRR190673/SRR190673.sra Written 15907024 spots for SRR190673/SRR190673.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: 00:02:33 15907024 reads; of these: 15907024 (100.00%) were unpaired; of these: 1688988 (10.62%) aligned 0 times 11629043 (73.11%) aligned exactly 1 time 2588993 (16.28%) aligned >1 times 89.38% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 4584587 / 14218036 = 0.3224 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 07:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.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 07:58:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:59: 1000000 INFO @ Tue, 16 Jun 2020 07:59:04: 2000000 INFO @ Tue, 16 Jun 2020 07:59:10: 3000000 INFO @ Tue, 16 Jun 2020 07:59:15: 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 07:59:21: 5000000 INFO @ Tue, 16 Jun 2020 07:59:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.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 07:59:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:27: 6000000 INFO @ Tue, 16 Jun 2020 07:59:29: 1000000 INFO @ Tue, 16 Jun 2020 07:59:33: 7000000 INFO @ Tue, 16 Jun 2020 07:59:37: 2000000 INFO @ Tue, 16 Jun 2020 07:59:39: 8000000 INFO @ Tue, 16 Jun 2020 07:59:43: 3000000 INFO @ Tue, 16 Jun 2020 07:59:45: 9000000 INFO @ Tue, 16 Jun 2020 07:59:49: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:59:49: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:59:49: #1 total tags in treatment: 9633449 INFO @ Tue, 16 Jun 2020 07:59:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:49: #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 07:59:49: #1 tags after filtering in treatment: 9633449 INFO @ Tue, 16 Jun 2020 07:59:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:50: #2 number of paired peaks: 1487 INFO @ Tue, 16 Jun 2020 07:59:50: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:50: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:50: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:50: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:50: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 07:59:50: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 16 Jun 2020 07:59:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.05_model.r INFO @ Tue, 16 Jun 2020 07:59:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:50: 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 07:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.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 07:59:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:57: 5000000 INFO @ Tue, 16 Jun 2020 07:59:59: 1000000 INFO @ Tue, 16 Jun 2020 08:00:03: 6000000 INFO @ Tue, 16 Jun 2020 08:00:05: 2000000 INFO @ Tue, 16 Jun 2020 08:00:10: 7000000 INFO @ Tue, 16 Jun 2020 08:00:11: 3000000 INFO @ Tue, 16 Jun 2020 08:00:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:17: 8000000 INFO @ Tue, 16 Jun 2020 08:00:18: 4000000 INFO @ Tue, 16 Jun 2020 08:00:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.05_summits.bed INFO @ Tue, 16 Jun 2020 08:00:23: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (4530 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:00:23: 9000000 INFO @ Tue, 16 Jun 2020 08:00:24: 5000000 INFO @ Tue, 16 Jun 2020 08:00:27: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:00:27: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:00:27: #1 total tags in treatment: 9633449 INFO @ Tue, 16 Jun 2020 08:00:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:27: #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 08:00:27: #1 tags after filtering in treatment: 9633449 INFO @ Tue, 16 Jun 2020 08:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:28: #2 number of paired peaks: 1487 INFO @ Tue, 16 Jun 2020 08:00:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:28: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 08:00:28: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 16 Jun 2020 08:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.10_model.r INFO @ Tue, 16 Jun 2020 08:00:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:29: 6000000 INFO @ Tue, 16 Jun 2020 08:00:35: 7000000 INFO @ Tue, 16 Jun 2020 08:00:40: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:00:46: 9000000 INFO @ Tue, 16 Jun 2020 08:00:49: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:00:49: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:00:49: #1 total tags in treatment: 9633449 INFO @ Tue, 16 Jun 2020 08:00:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:49: #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 08:00:50: #1 tags after filtering in treatment: 9633449 INFO @ Tue, 16 Jun 2020 08:00:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:50: #2 number of paired peaks: 1487 INFO @ Tue, 16 Jun 2020 08:00:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:51: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 08:00:51: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 16 Jun 2020 08:00:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.20_model.r INFO @ Tue, 16 Jun 2020 08:00:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.10_summits.bed INFO @ Tue, 16 Jun 2020 08:01:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3450 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:01:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059233/SRX059233.20_summits.bed INFO @ Tue, 16 Jun 2020 08:01:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2548 records, 4 fields): 4 millis CompletedMACS2peakCalling