Job ID = 6367017 SRX = SRX2599462 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:21:01 prefetch.2.10.7: 1) Downloading 'SRR5297106'... 2020-06-15T23:21:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:53 prefetch.2.10.7: 'SRR5297106' is valid 2020-06-15T23:21:53 prefetch.2.10.7: 1) 'SRR5297106' was downloaded successfully 2020-06-15T23:22:26 prefetch.2.10.7: 'SRR5297106' has 6 unresolved dependencies 2020-06-15T23:22:26 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T23:22:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:22:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:22:41 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:22:41 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T23:22:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:22:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:22:59 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:22:59 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T23:22:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:15 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:23:15 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T23:23:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:30 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:23:30 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T23:23:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:47 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:23:47 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T23:23:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:02 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 23182877 spots for SRR5297106/SRR5297106.sra Written 23182877 spots for SRR5297106/SRR5297106.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: 00:04:10 23182877 reads; of these: 23182877 (100.00%) were unpaired; of these: 948337 (4.09%) aligned 0 times 16381941 (70.66%) aligned exactly 1 time 5852599 (25.25%) aligned >1 times 95.91% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 4447738 / 22234540 = 0.2000 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 08:35:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.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 08:35:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:15: 1000000 INFO @ Tue, 16 Jun 2020 08:35:21: 2000000 INFO @ Tue, 16 Jun 2020 08:35:26: 3000000 INFO @ Tue, 16 Jun 2020 08:35:31: 4000000 INFO @ Tue, 16 Jun 2020 08:35:36: 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 08:35:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.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 08:35:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:41: 6000000 INFO @ Tue, 16 Jun 2020 08:35:46: 1000000 INFO @ Tue, 16 Jun 2020 08:35:47: 7000000 INFO @ Tue, 16 Jun 2020 08:35:52: 2000000 INFO @ Tue, 16 Jun 2020 08:35:52: 8000000 INFO @ Tue, 16 Jun 2020 08:35:57: 3000000 INFO @ Tue, 16 Jun 2020 08:35:58: 9000000 INFO @ Tue, 16 Jun 2020 08:36:03: 4000000 INFO @ Tue, 16 Jun 2020 08:36:04: 10000000 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 08:36:09: 5000000 INFO @ Tue, 16 Jun 2020 08:36:09: 11000000 INFO @ Tue, 16 Jun 2020 08:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.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 08:36:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:15: 6000000 INFO @ Tue, 16 Jun 2020 08:36:15: 12000000 INFO @ Tue, 16 Jun 2020 08:36:17: 1000000 INFO @ Tue, 16 Jun 2020 08:36:21: 7000000 INFO @ Tue, 16 Jun 2020 08:36:22: 13000000 INFO @ Tue, 16 Jun 2020 08:36:25: 2000000 INFO @ Tue, 16 Jun 2020 08:36:27: 8000000 INFO @ Tue, 16 Jun 2020 08:36:28: 14000000 INFO @ Tue, 16 Jun 2020 08:36:32: 3000000 INFO @ Tue, 16 Jun 2020 08:36:33: 9000000 INFO @ Tue, 16 Jun 2020 08:36:34: 15000000 INFO @ Tue, 16 Jun 2020 08:36:39: 4000000 INFO @ Tue, 16 Jun 2020 08:36:39: 10000000 INFO @ Tue, 16 Jun 2020 08:36:40: 16000000 INFO @ Tue, 16 Jun 2020 08:36:46: 11000000 INFO @ Tue, 16 Jun 2020 08:36:46: 17000000 INFO @ Tue, 16 Jun 2020 08:36:46: 5000000 INFO @ Tue, 16 Jun 2020 08:36:51: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:36:51: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:36:51: #1 total tags in treatment: 17786802 INFO @ Tue, 16 Jun 2020 08:36:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:51: #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 08:36:52: #1 tags after filtering in treatment: 17786802 INFO @ Tue, 16 Jun 2020 08:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:52: 12000000 INFO @ Tue, 16 Jun 2020 08:36:53: #2 number of paired peaks: 1414 INFO @ Tue, 16 Jun 2020 08:36:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:53: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 08:36:53: #2 alternative fragment length(s) may be 2,144,163 bps INFO @ Tue, 16 Jun 2020 08:36:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.05_model.r INFO @ Tue, 16 Jun 2020 08:36:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:53: 6000000 INFO @ Tue, 16 Jun 2020 08:36:58: 13000000 INFO @ Tue, 16 Jun 2020 08:37:01: 7000000 INFO @ Tue, 16 Jun 2020 08:37:04: 14000000 INFO @ Tue, 16 Jun 2020 08:37:08: 8000000 INFO @ Tue, 16 Jun 2020 08:37:10: 15000000 INFO @ Tue, 16 Jun 2020 08:37:15: 9000000 INFO @ Tue, 16 Jun 2020 08:37:17: 16000000 INFO @ Tue, 16 Jun 2020 08:37:22: 10000000 INFO @ Tue, 16 Jun 2020 08:37:23: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:28: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:37:28: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:37:28: #1 total tags in treatment: 17786802 INFO @ Tue, 16 Jun 2020 08:37:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:28: #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 08:37:28: #1 tags after filtering in treatment: 17786802 INFO @ Tue, 16 Jun 2020 08:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:29: #2 number of paired peaks: 1414 INFO @ Tue, 16 Jun 2020 08:37:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:29: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 08:37:29: #2 alternative fragment length(s) may be 2,144,163 bps INFO @ Tue, 16 Jun 2020 08:37:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.10_model.r INFO @ Tue, 16 Jun 2020 08:37:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:29: 11000000 INFO @ Tue, 16 Jun 2020 08:37:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:36: 12000000 INFO @ Tue, 16 Jun 2020 08:37:43: 13000000 INFO @ Tue, 16 Jun 2020 08:37:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3185 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:49: 14000000 INFO @ Tue, 16 Jun 2020 08:37:56: 15000000 INFO @ Tue, 16 Jun 2020 08:38:02: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:38:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:09: 17000000 INFO @ Tue, 16 Jun 2020 08:38:14: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:38:14: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:38:14: #1 total tags in treatment: 17786802 INFO @ Tue, 16 Jun 2020 08:38:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:14: #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 08:38:15: #1 tags after filtering in treatment: 17786802 INFO @ Tue, 16 Jun 2020 08:38:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:16: #2 number of paired peaks: 1414 INFO @ Tue, 16 Jun 2020 08:38:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:16: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 08:38:16: #2 alternative fragment length(s) may be 2,144,163 bps INFO @ Tue, 16 Jun 2020 08:38:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.20_model.r INFO @ Tue, 16 Jun 2020 08:38:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:38:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.10_summits.bed INFO @ Tue, 16 Jun 2020 08:38:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1348 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:38:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2599462/SRX2599462.20_summits.bed INFO @ Tue, 16 Jun 2020 08:39:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (408 records, 4 fields): 2 millis CompletedMACS2peakCalling