Job ID = 6366676 SRX = SRX2202788 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:56:29 prefetch.2.10.7: 1) Downloading 'SRR4319294'... 2020-06-15T22:56:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:12 prefetch.2.10.7: 'SRR4319294' is valid 2020-06-15T22:57:12 prefetch.2.10.7: 1) 'SRR4319294' was downloaded successfully 2020-06-15T22:57:45 prefetch.2.10.7: 'SRR4319294' has 6 unresolved dependencies 2020-06-15T22:57:45 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T22:57:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:02 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:58:02 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T22:58:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:18 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:58:18 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T22:58:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:34 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:58:34 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T22:58:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:50 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:58:50 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T22:58:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:07 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:59:07 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T22:59:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:24 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 24890077 spots for SRR4319294/SRR4319294.sra Written 24890077 spots for SRR4319294/SRR4319294.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: 00:05:04 24890077 reads; of these: 24890077 (100.00%) were unpaired; of these: 3597327 (14.45%) aligned 0 times 10585765 (42.53%) aligned exactly 1 time 10706985 (43.02%) aligned >1 times 85.55% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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_sort_core] merging from 12 files... [bam_rmdupse_core] 10124370 / 21292750 = 0.4755 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 08:09:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.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 08:09:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:05: 1000000 INFO @ Tue, 16 Jun 2020 08:10:10: 2000000 INFO @ Tue, 16 Jun 2020 08:10:16: 3000000 INFO @ Tue, 16 Jun 2020 08:10:21: 4000000 INFO @ Tue, 16 Jun 2020 08:10:27: 5000000 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 08:10:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.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 08:10:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:33: 6000000 INFO @ Tue, 16 Jun 2020 08:10:35: 1000000 INFO @ Tue, 16 Jun 2020 08:10:39: 7000000 INFO @ Tue, 16 Jun 2020 08:10:42: 2000000 INFO @ Tue, 16 Jun 2020 08:10:45: 8000000 INFO @ Tue, 16 Jun 2020 08:10:48: 3000000 INFO @ Tue, 16 Jun 2020 08:10:52: 9000000 INFO @ Tue, 16 Jun 2020 08:10:54: 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 08:10:58: 10000000 INFO @ Tue, 16 Jun 2020 08:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.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 08:11:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:00: 5000000 INFO @ Tue, 16 Jun 2020 08:11:05: 11000000 INFO @ Tue, 16 Jun 2020 08:11:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:06: #1 total tags in treatment: 11168380 INFO @ Tue, 16 Jun 2020 08:11:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:06: #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 08:11:06: #1 tags after filtering in treatment: 11168380 INFO @ Tue, 16 Jun 2020 08:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:06: 1000000 INFO @ Tue, 16 Jun 2020 08:11:06: 6000000 INFO @ Tue, 16 Jun 2020 08:11:07: #2 number of paired peaks: 1971 INFO @ Tue, 16 Jun 2020 08:11:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:07: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:11:07: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:11:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.05_model.r INFO @ Tue, 16 Jun 2020 08:11:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:12: 2000000 INFO @ Tue, 16 Jun 2020 08:11:13: 7000000 INFO @ Tue, 16 Jun 2020 08:11:18: 3000000 INFO @ Tue, 16 Jun 2020 08:11:19: 8000000 INFO @ Tue, 16 Jun 2020 08:11:25: 4000000 INFO @ Tue, 16 Jun 2020 08:11:25: 9000000 INFO @ Tue, 16 Jun 2020 08:11:31: 5000000 INFO @ Tue, 16 Jun 2020 08:11:31: 10000000 INFO @ Tue, 16 Jun 2020 08:11:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:37: 6000000 INFO @ Tue, 16 Jun 2020 08:11:38: 11000000 INFO @ Tue, 16 Jun 2020 08:11:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:39: #1 total tags in treatment: 11168380 INFO @ Tue, 16 Jun 2020 08:11:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:39: #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 08:11:39: #1 tags after filtering in treatment: 11168380 INFO @ Tue, 16 Jun 2020 08:11:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:40: #2 number of paired peaks: 1971 INFO @ Tue, 16 Jun 2020 08:11:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:40: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:11:40: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:11:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.10_model.r INFO @ Tue, 16 Jun 2020 08:11:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:43: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:49: 8000000 INFO @ Tue, 16 Jun 2020 08:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7628 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:55: 9000000 INFO @ Tue, 16 Jun 2020 08:12:01: 10000000 INFO @ Tue, 16 Jun 2020 08:12:07: 11000000 INFO @ Tue, 16 Jun 2020 08:12:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:08: #1 total tags in treatment: 11168380 INFO @ Tue, 16 Jun 2020 08:12:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:08: #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 08:12:08: #1 tags after filtering in treatment: 11168380 INFO @ Tue, 16 Jun 2020 08:12:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:09: #2 number of paired peaks: 1971 INFO @ Tue, 16 Jun 2020 08:12:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:09: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:12:09: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:12:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.20_model.r INFO @ Tue, 16 Jun 2020 08:12:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:12:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.10_summits.bed INFO @ Tue, 16 Jun 2020 08:12:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5002 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202788/SRX2202788.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2984 records, 4 fields): 4 millis CompletedMACS2peakCalling