Job ID = 6367877 SRX = SRX4107862 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:35:20 prefetch.2.10.7: 1) Downloading 'SRR7191138'... 2020-06-15T23:35:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:31 prefetch.2.10.7: 'SRR7191138' is valid 2020-06-15T23:36:31 prefetch.2.10.7: 1) 'SRR7191138' was downloaded successfully 2020-06-15T23:37:53 prefetch.2.10.7: 'SRR7191138' has 16 unresolved dependencies 2020-06-15T23:37:53 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_003279.8?vdb-ctx=refseq'... 2020-06-15T23:37:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:09 prefetch.2.10.7: 2) 'ncbi-acc:NC_003279.8?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:38:09 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_003280.10?vdb-ctx=refseq'... 2020-06-15T23:38:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:24 prefetch.2.10.7: 3) 'ncbi-acc:NC_003280.10?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:38:24 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_003281.10?vdb-ctx=refseq'... 2020-06-15T23:38:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:41 prefetch.2.10.7: 4) 'ncbi-acc:NC_003281.10?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:38:41 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_003282.8?vdb-ctx=refseq'... 2020-06-15T23:38:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:57 prefetch.2.10.7: 5) 'ncbi-acc:NC_003282.8?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:38:57 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_003283.11?vdb-ctx=refseq'... 2020-06-15T23:38:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:19 prefetch.2.10.7: 6) 'ncbi-acc:NC_003283.11?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:39:19 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NC_003284.9?vdb-ctx=refseq'... 2020-06-15T23:39:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:37 prefetch.2.10.7: 7) 'ncbi-acc:NC_003284.9?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:39:37 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NC_013486.1?vdb-ctx=refseq'... 2020-06-15T23:39:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:53 prefetch.2.10.7: 8) 'ncbi-acc:NC_013486.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:39:53 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NC_013487.1?vdb-ctx=refseq'... 2020-06-15T23:39:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:09 prefetch.2.10.7: 9) 'ncbi-acc:NC_013487.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:40:09 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NC_013488.1?vdb-ctx=refseq'... 2020-06-15T23:40:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:25 prefetch.2.10.7: 10) 'ncbi-acc:NC_013488.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:40:25 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NC_013489.1?vdb-ctx=refseq'... 2020-06-15T23:40:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:43 prefetch.2.10.7: 11) 'ncbi-acc:NC_013489.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:40:43 prefetch.2.10.7: 12) Downloading 'ncbi-acc:NC_013490.1?vdb-ctx=refseq'... 2020-06-15T23:40:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:58 prefetch.2.10.7: 12) 'ncbi-acc:NC_013490.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:40:58 prefetch.2.10.7: 13) Downloading 'ncbi-acc:NC_013491.1?vdb-ctx=refseq'... 2020-06-15T23:40:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:14 prefetch.2.10.7: 13) 'ncbi-acc:NC_013491.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:14 prefetch.2.10.7: 14) Downloading 'ncbi-acc:NW_003101683.1?vdb-ctx=refseq'... 2020-06-15T23:41:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:27 prefetch.2.10.7: 14) 'ncbi-acc:NW_003101683.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:27 prefetch.2.10.7: 15) Downloading 'ncbi-acc:NW_003101684.1?vdb-ctx=refseq'... 2020-06-15T23:41:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:40 prefetch.2.10.7: 15) 'ncbi-acc:NW_003101684.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:40 prefetch.2.10.7: 16) Downloading 'ncbi-acc:NW_003101687.1?vdb-ctx=refseq'... 2020-06-15T23:41:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:53 prefetch.2.10.7: 16) 'ncbi-acc:NW_003101687.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:53 prefetch.2.10.7: 17) Downloading 'ncbi-acc:NW_003101688.1?vdb-ctx=refseq'... 2020-06-15T23:41:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:07 prefetch.2.10.7: 17) 'ncbi-acc:NW_003101688.1?vdb-ctx=refseq' was downloaded successfully Read 14109239 spots for SRR7191138/SRR7191138.sra Written 14109239 spots for SRR7191138/SRR7191138.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: 00:01:59 14109239 reads; of these: 14109239 (100.00%) were unpaired; of these: 2180111 (15.45%) aligned 0 times 10644899 (75.45%) aligned exactly 1 time 1284229 (9.10%) aligned >1 times 84.55% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 2733748 / 11929128 = 0.2292 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 08:48:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.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 08:48:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:06: 1000000 INFO @ Tue, 16 Jun 2020 08:48:11: 2000000 INFO @ Tue, 16 Jun 2020 08:48:17: 3000000 INFO @ Tue, 16 Jun 2020 08:48:22: 4000000 INFO @ Tue, 16 Jun 2020 08:48:28: 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 08:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.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 08:48:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:33: 6000000 INFO @ Tue, 16 Jun 2020 08:48:36: 1000000 INFO @ Tue, 16 Jun 2020 08:48:39: 7000000 INFO @ Tue, 16 Jun 2020 08:48:42: 2000000 INFO @ Tue, 16 Jun 2020 08:48:45: 8000000 INFO @ Tue, 16 Jun 2020 08:48:48: 3000000 INFO @ Tue, 16 Jun 2020 08:48:51: 9000000 INFO @ Tue, 16 Jun 2020 08:48:52: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:48:52: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:48:52: #1 total tags in treatment: 9195380 INFO @ Tue, 16 Jun 2020 08:48:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:52: #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 08:48:52: #1 tags after filtering in treatment: 9195380 INFO @ Tue, 16 Jun 2020 08:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:53: #2 number of paired peaks: 6176 INFO @ Tue, 16 Jun 2020 08:48:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:53: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:48:53: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:48:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.05_model.r INFO @ Tue, 16 Jun 2020 08:48:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:54: 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 08:48:59: 5000000 INFO @ Tue, 16 Jun 2020 08:49:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.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 08:49:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:05: 6000000 INFO @ Tue, 16 Jun 2020 08:49:06: 1000000 INFO @ Tue, 16 Jun 2020 08:49:11: 7000000 INFO @ Tue, 16 Jun 2020 08:49:12: 2000000 INFO @ Tue, 16 Jun 2020 08:49:17: 8000000 INFO @ Tue, 16 Jun 2020 08:49:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:18: 3000000 INFO @ Tue, 16 Jun 2020 08:49:23: 9000000 INFO @ Tue, 16 Jun 2020 08:49:24: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:49:24: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:49:24: #1 total tags in treatment: 9195380 INFO @ Tue, 16 Jun 2020 08:49:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:24: #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 08:49:24: #1 tags after filtering in treatment: 9195380 INFO @ Tue, 16 Jun 2020 08:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:24: 4000000 INFO @ Tue, 16 Jun 2020 08:49:25: #2 number of paired peaks: 6176 INFO @ Tue, 16 Jun 2020 08:49:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:25: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:49:25: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.10_model.r INFO @ Tue, 16 Jun 2020 08:49:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:30: 5000000 INFO @ Tue, 16 Jun 2020 08:49:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.05_summits.bed INFO @ Tue, 16 Jun 2020 08:49:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6883 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:35: 6000000 INFO @ Tue, 16 Jun 2020 08:49:40: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:49:46: 8000000 INFO @ Tue, 16 Jun 2020 08:49:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:51: 9000000 INFO @ Tue, 16 Jun 2020 08:49:52: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:49:52: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:49:52: #1 total tags in treatment: 9195380 INFO @ Tue, 16 Jun 2020 08:49:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:52: #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 08:49:52: #1 tags after filtering in treatment: 9195380 INFO @ Tue, 16 Jun 2020 08:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:53: #2 number of paired peaks: 6176 INFO @ Tue, 16 Jun 2020 08:49:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:54: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:49:54: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.20_model.r INFO @ Tue, 16 Jun 2020 08:49:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5561 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:50:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107862/SRX4107862.20_summits.bed INFO @ Tue, 16 Jun 2020 08:50:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4528 records, 4 fields): 8 millis CompletedMACS2peakCalling