Job ID = 6366664 SRX = SRX2202775 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:55:29 prefetch.2.10.7: 1) Downloading 'SRR4319281'... 2020-06-15T22:55:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:25 prefetch.2.10.7: 'SRR4319281' is valid 2020-06-15T22:56:25 prefetch.2.10.7: 1) 'SRR4319281' was downloaded successfully 2020-06-15T22:56:58 prefetch.2.10.7: 'SRR4319281' has 6 unresolved dependencies 2020-06-15T22:56:58 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T22:56:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:14 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:57:14 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T22:57:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:29 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:57:29 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T22:57:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:45 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:57:45 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T22:57:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:01 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:58:01 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T22:58:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:17 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:58:17 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T22:58:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:33 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 16937099 spots for SRR4319281/SRR4319281.sra Written 16937099 spots for SRR4319281/SRR4319281.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: 00:03:41 16937099 reads; of these: 16937099 (100.00%) were unpaired; of these: 2404055 (14.19%) aligned 0 times 8460706 (49.95%) aligned exactly 1 time 6072338 (35.85%) aligned >1 times 85.81% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4419618 / 14533044 = 0.3041 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 08:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.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 08:06:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:36: 1000000 INFO @ Tue, 16 Jun 2020 08:06:41: 2000000 INFO @ Tue, 16 Jun 2020 08:06:46: 3000000 INFO @ Tue, 16 Jun 2020 08:06:51: 4000000 INFO @ Tue, 16 Jun 2020 08:06:56: 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 08:07:01: 6000000 INFO @ Tue, 16 Jun 2020 08:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.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 08:07:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:05: 7000000 INFO @ Tue, 16 Jun 2020 08:07:07: 1000000 INFO @ Tue, 16 Jun 2020 08:07:10: 8000000 INFO @ Tue, 16 Jun 2020 08:07:12: 2000000 INFO @ Tue, 16 Jun 2020 08:07:15: 9000000 INFO @ Tue, 16 Jun 2020 08:07:17: 3000000 INFO @ Tue, 16 Jun 2020 08:07:20: 10000000 INFO @ Tue, 16 Jun 2020 08:07:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:21: #1 total tags in treatment: 10113426 INFO @ Tue, 16 Jun 2020 08:07:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:21: #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 08:07:21: #1 tags after filtering in treatment: 10113426 INFO @ Tue, 16 Jun 2020 08:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:21: 4000000 INFO @ Tue, 16 Jun 2020 08:07:22: #2 number of paired peaks: 2707 INFO @ Tue, 16 Jun 2020 08:07:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:22: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 08:07:22: #2 alternative fragment length(s) may be 3,119 bps INFO @ Tue, 16 Jun 2020 08:07:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.05_model.r INFO @ Tue, 16 Jun 2020 08:07:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:26: 5000000 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 08:07:31: 6000000 INFO @ Tue, 16 Jun 2020 08:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.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 08:07:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:36: 7000000 INFO @ Tue, 16 Jun 2020 08:07:37: 1000000 INFO @ Tue, 16 Jun 2020 08:07:41: 2000000 INFO @ Tue, 16 Jun 2020 08:07:41: 8000000 INFO @ Tue, 16 Jun 2020 08:07:46: 3000000 INFO @ Tue, 16 Jun 2020 08:07:46: 9000000 INFO @ Tue, 16 Jun 2020 08:07:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:51: 4000000 INFO @ Tue, 16 Jun 2020 08:07:51: 10000000 INFO @ Tue, 16 Jun 2020 08:07:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:52: #1 total tags in treatment: 10113426 INFO @ Tue, 16 Jun 2020 08:07:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:52: #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 08:07:52: #1 tags after filtering in treatment: 10113426 INFO @ Tue, 16 Jun 2020 08:07:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:53: #2 number of paired peaks: 2707 INFO @ Tue, 16 Jun 2020 08:07:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:53: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 08:07:53: #2 alternative fragment length(s) may be 3,119 bps INFO @ Tue, 16 Jun 2020 08:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.10_model.r INFO @ Tue, 16 Jun 2020 08:07:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:56: 5000000 INFO @ Tue, 16 Jun 2020 08:08:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:01: Done! INFO @ Tue, 16 Jun 2020 08:08:01: 6000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4581 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:06: 7000000 INFO @ Tue, 16 Jun 2020 08:08:10: 8000000 INFO @ Tue, 16 Jun 2020 08:08:15: 9000000 INFO @ Tue, 16 Jun 2020 08:08:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:20: 10000000 INFO @ Tue, 16 Jun 2020 08:08:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:08:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:08:20: #1 total tags in treatment: 10113426 INFO @ Tue, 16 Jun 2020 08:08:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:20: #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 08:08:20: #1 tags after filtering in treatment: 10113426 INFO @ Tue, 16 Jun 2020 08:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:21: #2 number of paired peaks: 2707 INFO @ Tue, 16 Jun 2020 08:08:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:21: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 08:08:21: #2 alternative fragment length(s) may be 3,119 bps INFO @ Tue, 16 Jun 2020 08:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.20_model.r INFO @ Tue, 16 Jun 2020 08:08:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2355 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:08:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202775/SRX2202775.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (914 records, 4 fields): 2 millis CompletedMACS2peakCalling