Job ID = 6367878 SRX = SRX4107863 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:46:14 prefetch.2.10.7: 1) Downloading 'SRR7191139'... 2020-06-15T23:46:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:58 prefetch.2.10.7: 'SRR7191139' is valid 2020-06-15T23:46:58 prefetch.2.10.7: 1) 'SRR7191139' was downloaded successfully 2020-06-15T23:48:18 prefetch.2.10.7: 'SRR7191139' has 16 unresolved dependencies 2020-06-15T23:48:18 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_003279.8?vdb-ctx=refseq'... 2020-06-15T23:48:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:35 prefetch.2.10.7: 2) 'ncbi-acc:NC_003279.8?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:48:35 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_003280.10?vdb-ctx=refseq'... 2020-06-15T23:48:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:59 prefetch.2.10.7: 3) 'ncbi-acc:NC_003280.10?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:48:59 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_003281.10?vdb-ctx=refseq'... 2020-06-15T23:48:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:16 prefetch.2.10.7: 4) 'ncbi-acc:NC_003281.10?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:49:16 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_003282.8?vdb-ctx=refseq'... 2020-06-15T23:49:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:32 prefetch.2.10.7: 5) 'ncbi-acc:NC_003282.8?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:49:32 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_003283.11?vdb-ctx=refseq'... 2020-06-15T23:49:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:50 prefetch.2.10.7: 6) 'ncbi-acc:NC_003283.11?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:49:50 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NC_003284.9?vdb-ctx=refseq'... 2020-06-15T23:49:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:07 prefetch.2.10.7: 7) 'ncbi-acc:NC_003284.9?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:50:07 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NC_013486.1?vdb-ctx=refseq'... 2020-06-15T23:50:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:24 prefetch.2.10.7: 8) 'ncbi-acc:NC_013486.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:50:24 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NC_013487.1?vdb-ctx=refseq'... 2020-06-15T23:50:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:43 prefetch.2.10.7: 9) 'ncbi-acc:NC_013487.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:50:43 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NC_013488.1?vdb-ctx=refseq'... 2020-06-15T23:50:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:00 prefetch.2.10.7: 10) 'ncbi-acc:NC_013488.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:51:00 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NC_013489.1?vdb-ctx=refseq'... 2020-06-15T23:51:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:15 prefetch.2.10.7: 11) 'ncbi-acc:NC_013489.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:51:15 prefetch.2.10.7: 12) Downloading 'ncbi-acc:NC_013490.1?vdb-ctx=refseq'... 2020-06-15T23:51:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:30 prefetch.2.10.7: 12) 'ncbi-acc:NC_013490.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:51:30 prefetch.2.10.7: 13) Downloading 'ncbi-acc:NC_013491.1?vdb-ctx=refseq'... 2020-06-15T23:51:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:48 prefetch.2.10.7: 13) 'ncbi-acc:NC_013491.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:51:48 prefetch.2.10.7: 14) Downloading 'ncbi-acc:NW_003101683.1?vdb-ctx=refseq'... 2020-06-15T23:51:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:03 prefetch.2.10.7: 14) 'ncbi-acc:NW_003101683.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:52:03 prefetch.2.10.7: 15) Downloading 'ncbi-acc:NW_003101684.1?vdb-ctx=refseq'... 2020-06-15T23:52:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:16 prefetch.2.10.7: 15) 'ncbi-acc:NW_003101684.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:52:16 prefetch.2.10.7: 16) Downloading 'ncbi-acc:NW_003101687.1?vdb-ctx=refseq'... 2020-06-15T23:52:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:29 prefetch.2.10.7: 16) 'ncbi-acc:NW_003101687.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:52:29 prefetch.2.10.7: 17) Downloading 'ncbi-acc:NW_003101688.1?vdb-ctx=refseq'... 2020-06-15T23:52:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:45 prefetch.2.10.7: 17) 'ncbi-acc:NW_003101688.1?vdb-ctx=refseq' was downloaded successfully Read 13293366 spots for SRR7191139/SRR7191139.sra Written 13293366 spots for SRR7191139/SRR7191139.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: 00:02:01 13293366 reads; of these: 13293366 (100.00%) were unpaired; of these: 2024693 (15.23%) aligned 0 times 10066843 (75.73%) aligned exactly 1 time 1201830 (9.04%) aligned >1 times 84.77% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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] 4068092 / 11268673 = 0.3610 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 08:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.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 08:58:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:14: 1000000 INFO @ Tue, 16 Jun 2020 08:58:18: 2000000 INFO @ Tue, 16 Jun 2020 08:58:23: 3000000 INFO @ Tue, 16 Jun 2020 08:58:27: 4000000 INFO @ Tue, 16 Jun 2020 08:58:32: 5000000 INFO @ Tue, 16 Jun 2020 08:58:37: 6000000 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 08:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.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 08:58:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:41: 7000000 INFO @ Tue, 16 Jun 2020 08:58:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:58:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:58:42: #1 total tags in treatment: 7200581 INFO @ Tue, 16 Jun 2020 08:58:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:42: #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 08:58:42: #1 tags after filtering in treatment: 7200581 INFO @ Tue, 16 Jun 2020 08:58:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:43: #2 number of paired peaks: 6191 INFO @ Tue, 16 Jun 2020 08:58:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:43: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 08:58:43: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 08:58:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.05_model.r INFO @ Tue, 16 Jun 2020 08:58:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:43: 1000000 INFO @ Tue, 16 Jun 2020 08:58:48: 2000000 INFO @ Tue, 16 Jun 2020 08:58:52: 3000000 INFO @ Tue, 16 Jun 2020 08:58:57: 4000000 INFO @ Tue, 16 Jun 2020 08:59:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:02: 5000000 INFO @ Tue, 16 Jun 2020 08:59:06: 6000000 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 08:59:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.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 08:59:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.05_summits.bed INFO @ Tue, 16 Jun 2020 08:59:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6862 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:59:11: 7000000 INFO @ Tue, 16 Jun 2020 08:59:12: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:59:12: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:59:12: #1 total tags in treatment: 7200581 INFO @ Tue, 16 Jun 2020 08:59:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:12: #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 08:59:12: #1 tags after filtering in treatment: 7200581 INFO @ Tue, 16 Jun 2020 08:59:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:13: #2 number of paired peaks: 6191 INFO @ Tue, 16 Jun 2020 08:59:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:13: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 08:59:13: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 08:59:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.10_model.r INFO @ Tue, 16 Jun 2020 08:59:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:14: 1000000 INFO @ Tue, 16 Jun 2020 08:59:20: 2000000 INFO @ Tue, 16 Jun 2020 08:59:25: 3000000 INFO @ Tue, 16 Jun 2020 08:59:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:31: 4000000 INFO @ Tue, 16 Jun 2020 08:59:36: 5000000 INFO @ Tue, 16 Jun 2020 08:59:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.10_summits.bed INFO @ Tue, 16 Jun 2020 08:59:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5607 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:59:42: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:59:47: 7000000 INFO @ Tue, 16 Jun 2020 08:59:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:59:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:59:48: #1 total tags in treatment: 7200581 INFO @ Tue, 16 Jun 2020 08:59:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:48: #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 08:59:48: #1 tags after filtering in treatment: 7200581 INFO @ Tue, 16 Jun 2020 08:59:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:49: #2 number of paired peaks: 6191 INFO @ Tue, 16 Jun 2020 08:59:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:49: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 08:59:49: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 16 Jun 2020 08:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.20_model.r INFO @ Tue, 16 Jun 2020 08:59:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:00:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107863/SRX4107863.20_summits.bed INFO @ Tue, 16 Jun 2020 09:00:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4502 records, 4 fields): 5 millis CompletedMACS2peakCalling