Job ID = 6367882 SRX = SRX4107867 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:57:50 prefetch.2.10.7: 1) Downloading 'SRR7191143'... 2020-06-15T23:57:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:58:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:58:25 prefetch.2.10.7: 'SRR7191143' is valid 2020-06-15T23:58:25 prefetch.2.10.7: 1) 'SRR7191143' was downloaded successfully 2020-06-15T23:59:45 prefetch.2.10.7: 'SRR7191143' has 16 unresolved dependencies 2020-06-15T23:59:45 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_003279.8?vdb-ctx=refseq'... 2020-06-15T23:59:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:14 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:14 prefetch.2.10.7: 2) 'ncbi-acc:NC_003279.8?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:00:14 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_003280.10?vdb-ctx=refseq'... 2020-06-16T00:00:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:31 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:31 prefetch.2.10.7: 3) 'ncbi-acc:NC_003280.10?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:00:31 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_003281.10?vdb-ctx=refseq'... 2020-06-16T00:00:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:46 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:46 prefetch.2.10.7: 4) 'ncbi-acc:NC_003281.10?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:00:46 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_003282.8?vdb-ctx=refseq'... 2020-06-16T00:00:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:03 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:03 prefetch.2.10.7: 5) 'ncbi-acc:NC_003282.8?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:01:03 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_003283.11?vdb-ctx=refseq'... 2020-06-16T00:01:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:19 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:19 prefetch.2.10.7: 6) 'ncbi-acc:NC_003283.11?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:01:19 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NC_003284.9?vdb-ctx=refseq'... 2020-06-16T00:01:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:36 prefetch.2.10.7: 7) 'ncbi-acc:NC_003284.9?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:01:36 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NC_013486.1?vdb-ctx=refseq'... 2020-06-16T00:01:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:52 prefetch.2.10.7: 8) 'ncbi-acc:NC_013486.1?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:01:52 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NC_013487.1?vdb-ctx=refseq'... 2020-06-16T00:01:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:03:55 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:03:55 prefetch.2.10.7: 9) 'ncbi-acc:NC_013487.1?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:03:55 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NC_013488.1?vdb-ctx=refseq'... 2020-06-16T00:03:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:04:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:04:13 prefetch.2.10.7: 10) 'ncbi-acc:NC_013488.1?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:04:13 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NC_013489.1?vdb-ctx=refseq'... 2020-06-16T00:04:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:04:28 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:04:28 prefetch.2.10.7: 11) 'ncbi-acc:NC_013489.1?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:04:28 prefetch.2.10.7: 12) Downloading 'ncbi-acc:NC_013490.1?vdb-ctx=refseq'... 2020-06-16T00:04:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:04:44 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:04:44 prefetch.2.10.7: 12) 'ncbi-acc:NC_013490.1?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:04:44 prefetch.2.10.7: 13) Downloading 'ncbi-acc:NC_013491.1?vdb-ctx=refseq'... 2020-06-16T00:04:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:00 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:00 prefetch.2.10.7: 13) 'ncbi-acc:NC_013491.1?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:05:00 prefetch.2.10.7: 14) Downloading 'ncbi-acc:NW_003101683.1?vdb-ctx=refseq'... 2020-06-16T00:05:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:13 prefetch.2.10.7: 14) 'ncbi-acc:NW_003101683.1?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:05:13 prefetch.2.10.7: 15) Downloading 'ncbi-acc:NW_003101684.1?vdb-ctx=refseq'... 2020-06-16T00:05:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:25 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:25 prefetch.2.10.7: 15) 'ncbi-acc:NW_003101684.1?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:05:25 prefetch.2.10.7: 16) Downloading 'ncbi-acc:NW_003101687.1?vdb-ctx=refseq'... 2020-06-16T00:05:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:39 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:39 prefetch.2.10.7: 16) 'ncbi-acc:NW_003101687.1?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:05:39 prefetch.2.10.7: 17) Downloading 'ncbi-acc:NW_003101688.1?vdb-ctx=refseq'... 2020-06-16T00:05:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:54 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:54 prefetch.2.10.7: 17) 'ncbi-acc:NW_003101688.1?vdb-ctx=refseq' was downloaded successfully Read 16335185 spots for SRR7191143/SRR7191143.sra Written 16335185 spots for SRR7191143/SRR7191143.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: 00:02:11 16335185 reads; of these: 16335185 (100.00%) were unpaired; of these: 7026505 (43.01%) aligned 0 times 7434706 (45.51%) aligned exactly 1 time 1873974 (11.47%) aligned >1 times 56.99% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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_rmdupse_core] 1356930 / 9308680 = 0.1458 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 09:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.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 09:11:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:36: 1000000 INFO @ Tue, 16 Jun 2020 09:11:41: 2000000 INFO @ Tue, 16 Jun 2020 09:11:46: 3000000 INFO @ Tue, 16 Jun 2020 09:11:51: 4000000 INFO @ Tue, 16 Jun 2020 09:11:57: 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 09:12:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.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 09:12:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:02: 6000000 INFO @ Tue, 16 Jun 2020 09:12:06: 1000000 INFO @ Tue, 16 Jun 2020 09:12:08: 7000000 INFO @ Tue, 16 Jun 2020 09:12:12: 2000000 INFO @ Tue, 16 Jun 2020 09:12:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:13: #1 total tags in treatment: 7951750 INFO @ Tue, 16 Jun 2020 09:12:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:13: #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 09:12:14: #1 tags after filtering in treatment: 7951750 INFO @ Tue, 16 Jun 2020 09:12:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:14: #2 number of paired peaks: 2245 INFO @ Tue, 16 Jun 2020 09:12:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:14: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:12:14: #2 alternative fragment length(s) may be 144,595 bps INFO @ Tue, 16 Jun 2020 09:12:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.05_model.r INFO @ Tue, 16 Jun 2020 09:12:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:18: 3000000 INFO @ Tue, 16 Jun 2020 09:12:23: 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 09:12:29: 5000000 INFO @ Tue, 16 Jun 2020 09:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.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 09:12:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:35: 6000000 INFO @ Tue, 16 Jun 2020 09:12:36: 1000000 INFO @ Tue, 16 Jun 2020 09:12:40: 7000000 INFO @ Tue, 16 Jun 2020 09:12:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:42: Done! INFO @ Tue, 16 Jun 2020 09:12:42: 2000000 pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6928 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:46: #1 total tags in treatment: 7951750 INFO @ Tue, 16 Jun 2020 09:12:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:46: #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 09:12:46: #1 tags after filtering in treatment: 7951750 INFO @ Tue, 16 Jun 2020 09:12:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:47: #2 number of paired peaks: 2245 INFO @ Tue, 16 Jun 2020 09:12:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:47: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:12:47: #2 alternative fragment length(s) may be 144,595 bps INFO @ Tue, 16 Jun 2020 09:12:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.10_model.r INFO @ Tue, 16 Jun 2020 09:12:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:47: 3000000 INFO @ Tue, 16 Jun 2020 09:12:53: 4000000 INFO @ Tue, 16 Jun 2020 09:12:59: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:04: 6000000 INFO @ Tue, 16 Jun 2020 09:13:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:10: 7000000 INFO @ Tue, 16 Jun 2020 09:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3814 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:13:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:13:15: #1 total tags in treatment: 7951750 INFO @ Tue, 16 Jun 2020 09:13:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:15: #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 09:13:15: #1 tags after filtering in treatment: 7951750 INFO @ Tue, 16 Jun 2020 09:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:16: #2 number of paired peaks: 2245 INFO @ Tue, 16 Jun 2020 09:13:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:16: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:13:16: #2 alternative fragment length(s) may be 144,595 bps INFO @ Tue, 16 Jun 2020 09:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.20_model.r INFO @ Tue, 16 Jun 2020 09:13:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107867/SRX4107867.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1692 records, 4 fields): 2 millis CompletedMACS2peakCalling