Job ID = 6366673 SRX = SRX2202786 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:31 prefetch.2.10.7: 1) Downloading 'SRR4319292'... 2020-06-15T23:10:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:40 prefetch.2.10.7: 'SRR4319292' is valid 2020-06-15T23:11:40 prefetch.2.10.7: 1) 'SRR4319292' was downloaded successfully 2020-06-15T23:12:13 prefetch.2.10.7: 'SRR4319292' has 6 unresolved dependencies 2020-06-15T23:12:13 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T23:12:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:30 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:12:30 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T23:12:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:46 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:12:46 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T23:12:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:01 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:13:01 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T23:13:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:16 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:13:16 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T23:13:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:33 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:13:33 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T23:13:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:49 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:49 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 19485470 spots for SRR4319292/SRR4319292.sra Written 19485470 spots for SRR4319292/SRR4319292.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: 00:03:49 19485470 reads; of these: 19485470 (100.00%) were unpaired; of these: 1793200 (9.20%) aligned 0 times 12293737 (63.09%) aligned exactly 1 time 5398533 (27.71%) aligned >1 times 90.80% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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 8 files... [bam_rmdupse_core] 4222048 / 17692270 = 0.2386 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 08:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.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 08:22:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:05: 1000000 INFO @ Tue, 16 Jun 2020 08:23:11: 2000000 INFO @ Tue, 16 Jun 2020 08:23:17: 3000000 INFO @ Tue, 16 Jun 2020 08:23:22: 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 08:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.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 08:23:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:28: 5000000 INFO @ Tue, 16 Jun 2020 08:23:35: 1000000 INFO @ Tue, 16 Jun 2020 08:23:35: 6000000 INFO @ Tue, 16 Jun 2020 08:23:41: 7000000 INFO @ Tue, 16 Jun 2020 08:23:42: 2000000 INFO @ Tue, 16 Jun 2020 08:23:48: 8000000 INFO @ Tue, 16 Jun 2020 08:23:48: 3000000 INFO @ Tue, 16 Jun 2020 08:23:54: 9000000 INFO @ Tue, 16 Jun 2020 08:23:54: 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 08:23:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.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 08:23:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:01: 10000000 INFO @ Tue, 16 Jun 2020 08:24:01: 5000000 INFO @ Tue, 16 Jun 2020 08:24:05: 1000000 INFO @ Tue, 16 Jun 2020 08:24:07: 11000000 INFO @ Tue, 16 Jun 2020 08:24:08: 6000000 INFO @ Tue, 16 Jun 2020 08:24:12: 2000000 INFO @ Tue, 16 Jun 2020 08:24:14: 12000000 INFO @ Tue, 16 Jun 2020 08:24:15: 7000000 INFO @ Tue, 16 Jun 2020 08:24:19: 3000000 INFO @ Tue, 16 Jun 2020 08:24:21: 13000000 INFO @ Tue, 16 Jun 2020 08:24:21: 8000000 INFO @ Tue, 16 Jun 2020 08:24:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:24:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:24:24: #1 total tags in treatment: 13470222 INFO @ Tue, 16 Jun 2020 08:24:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:24: #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 08:24:24: #1 tags after filtering in treatment: 13470222 INFO @ Tue, 16 Jun 2020 08:24:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:25: #2 number of paired peaks: 1819 INFO @ Tue, 16 Jun 2020 08:24:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:25: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 08:24:25: #2 alternative fragment length(s) may be 4,119 bps INFO @ Tue, 16 Jun 2020 08:24:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.05_model.r INFO @ Tue, 16 Jun 2020 08:24:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:26: 4000000 INFO @ Tue, 16 Jun 2020 08:24:28: 9000000 INFO @ Tue, 16 Jun 2020 08:24:33: 5000000 INFO @ Tue, 16 Jun 2020 08:24:35: 10000000 INFO @ Tue, 16 Jun 2020 08:24:40: 6000000 INFO @ Tue, 16 Jun 2020 08:24:42: 11000000 INFO @ Tue, 16 Jun 2020 08:24:47: 7000000 INFO @ Tue, 16 Jun 2020 08:24:49: 12000000 INFO @ Tue, 16 Jun 2020 08:24:54: 8000000 INFO @ Tue, 16 Jun 2020 08:24:57: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:24:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:00: #1 total tags in treatment: 13470222 INFO @ Tue, 16 Jun 2020 08:25:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:00: #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 08:25:00: #1 tags after filtering in treatment: 13470222 INFO @ Tue, 16 Jun 2020 08:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:01: 9000000 INFO @ Tue, 16 Jun 2020 08:25:01: #2 number of paired peaks: 1819 INFO @ Tue, 16 Jun 2020 08:25:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:01: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 08:25:01: #2 alternative fragment length(s) may be 4,119 bps INFO @ Tue, 16 Jun 2020 08:25:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.10_model.r INFO @ Tue, 16 Jun 2020 08:25:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:07: 10000000 INFO @ Tue, 16 Jun 2020 08:25:14: 11000000 INFO @ Tue, 16 Jun 2020 08:25:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.05_summits.bed INFO @ Tue, 16 Jun 2020 08:25:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7690 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:20: 12000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:27: 13000000 INFO @ Tue, 16 Jun 2020 08:25:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:30: #1 total tags in treatment: 13470222 INFO @ Tue, 16 Jun 2020 08:25:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:30: #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 08:25:30: #1 tags after filtering in treatment: 13470222 INFO @ Tue, 16 Jun 2020 08:25:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:31: #2 number of paired peaks: 1819 INFO @ Tue, 16 Jun 2020 08:25:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:31: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 08:25:31: #2 alternative fragment length(s) may be 4,119 bps INFO @ Tue, 16 Jun 2020 08:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.20_model.r INFO @ Tue, 16 Jun 2020 08:25:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.10_summits.bed INFO @ Tue, 16 Jun 2020 08:25:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4132 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202786/SRX2202786.20_summits.bed INFO @ Tue, 16 Jun 2020 08:26:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1821 records, 4 fields): 3 millis CompletedMACS2peakCalling