Job ID = 6367880 SRX = SRX4107865 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:36:29 prefetch.2.10.7: 1) Downloading 'SRR7191141'... 2020-06-15T23:36:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:52 prefetch.2.10.7: 'SRR7191141' is valid 2020-06-15T23:37:52 prefetch.2.10.7: 1) 'SRR7191141' was downloaded successfully 2020-06-15T23:39:12 prefetch.2.10.7: 'SRR7191141' has 16 unresolved dependencies 2020-06-15T23:39:12 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_003279.8?vdb-ctx=refseq'... 2020-06-15T23:39:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:27 prefetch.2.10.7: 2) 'ncbi-acc:NC_003279.8?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:39:27 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_003280.10?vdb-ctx=refseq'... 2020-06-15T23:39:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:42 prefetch.2.10.7: 3) 'ncbi-acc:NC_003280.10?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:39:42 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_003281.10?vdb-ctx=refseq'... 2020-06-15T23:39:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:58 prefetch.2.10.7: 4) 'ncbi-acc:NC_003281.10?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:39:58 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_003282.8?vdb-ctx=refseq'... 2020-06-15T23:39:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:15 prefetch.2.10.7: 5) 'ncbi-acc:NC_003282.8?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:40:15 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_003283.11?vdb-ctx=refseq'... 2020-06-15T23:40:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:31 prefetch.2.10.7: 6) 'ncbi-acc:NC_003283.11?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:40:31 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NC_003284.9?vdb-ctx=refseq'... 2020-06-15T23:40:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:47 prefetch.2.10.7: 7) 'ncbi-acc:NC_003284.9?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:40:47 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NC_013486.1?vdb-ctx=refseq'... 2020-06-15T23:40:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:04 prefetch.2.10.7: 8) 'ncbi-acc:NC_013486.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:04 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NC_013487.1?vdb-ctx=refseq'... 2020-06-15T23:41:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:20 prefetch.2.10.7: 9) 'ncbi-acc:NC_013487.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:20 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NC_013488.1?vdb-ctx=refseq'... 2020-06-15T23:41:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:36 prefetch.2.10.7: 10) 'ncbi-acc:NC_013488.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:36 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NC_013489.1?vdb-ctx=refseq'... 2020-06-15T23:41:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:50 prefetch.2.10.7: 11) 'ncbi-acc:NC_013489.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:41:50 prefetch.2.10.7: 12) Downloading 'ncbi-acc:NC_013490.1?vdb-ctx=refseq'... 2020-06-15T23:41:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:06 prefetch.2.10.7: 12) 'ncbi-acc:NC_013490.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:42:06 prefetch.2.10.7: 13) Downloading 'ncbi-acc:NC_013491.1?vdb-ctx=refseq'... 2020-06-15T23:42:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:22 prefetch.2.10.7: 13) 'ncbi-acc:NC_013491.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:42:22 prefetch.2.10.7: 14) Downloading 'ncbi-acc:NW_003101683.1?vdb-ctx=refseq'... 2020-06-15T23:42:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:36 prefetch.2.10.7: 14) 'ncbi-acc:NW_003101683.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:42:36 prefetch.2.10.7: 15) Downloading 'ncbi-acc:NW_003101684.1?vdb-ctx=refseq'... 2020-06-15T23:42:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:50 prefetch.2.10.7: 15) 'ncbi-acc:NW_003101684.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:42:50 prefetch.2.10.7: 16) Downloading 'ncbi-acc:NW_003101687.1?vdb-ctx=refseq'... 2020-06-15T23:42:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:43:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:43:04 prefetch.2.10.7: 16) 'ncbi-acc:NW_003101687.1?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:43:04 prefetch.2.10.7: 17) Downloading 'ncbi-acc:NW_003101688.1?vdb-ctx=refseq'... 2020-06-15T23:43:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:43:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:43:18 prefetch.2.10.7: 17) 'ncbi-acc:NW_003101688.1?vdb-ctx=refseq' was downloaded successfully Read 19322666 spots for SRR7191141/SRR7191141.sra Written 19322666 spots for SRR7191141/SRR7191141.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: 00:02:44 19322666 reads; of these: 19322666 (100.00%) were unpaired; of these: 7280391 (37.68%) aligned 0 times 9643838 (49.91%) aligned exactly 1 time 2398437 (12.41%) aligned >1 times 62.32% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 2245448 / 12042275 = 0.1865 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 08:50:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.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 08:50:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:14: 1000000 INFO @ Tue, 16 Jun 2020 08:50:19: 2000000 INFO @ Tue, 16 Jun 2020 08:50:23: 3000000 INFO @ Tue, 16 Jun 2020 08:50:28: 4000000 INFO @ Tue, 16 Jun 2020 08:50:32: 5000000 INFO @ Tue, 16 Jun 2020 08:50:37: 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 08:50:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.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 08:50:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:42: 7000000 INFO @ Tue, 16 Jun 2020 08:50:45: 1000000 INFO @ Tue, 16 Jun 2020 08:50:46: 8000000 INFO @ Tue, 16 Jun 2020 08:50:50: 2000000 INFO @ Tue, 16 Jun 2020 08:50:51: 9000000 INFO @ Tue, 16 Jun 2020 08:50:55: 3000000 INFO @ Tue, 16 Jun 2020 08:50:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:55: #1 total tags in treatment: 9796827 INFO @ Tue, 16 Jun 2020 08:50:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:55: #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 08:50:56: #1 tags after filtering in treatment: 9796827 INFO @ Tue, 16 Jun 2020 08:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:56: #2 number of paired peaks: 1892 INFO @ Tue, 16 Jun 2020 08:50:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:56: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:50:56: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:50:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.05_model.r INFO @ Tue, 16 Jun 2020 08:50:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:00: 4000000 INFO @ Tue, 16 Jun 2020 08:51:05: 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 08:51:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.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 08:51:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:11: 6000000 INFO @ Tue, 16 Jun 2020 08:51:15: 1000000 INFO @ Tue, 16 Jun 2020 08:51:16: 7000000 INFO @ Tue, 16 Jun 2020 08:51:20: 2000000 INFO @ Tue, 16 Jun 2020 08:51:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:21: 8000000 INFO @ Tue, 16 Jun 2020 08:51:26: 3000000 INFO @ Tue, 16 Jun 2020 08:51:27: 9000000 INFO @ Tue, 16 Jun 2020 08:51:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:31: #1 total tags in treatment: 9796827 INFO @ Tue, 16 Jun 2020 08:51:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:31: #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 08:51:31: 4000000 INFO @ Tue, 16 Jun 2020 08:51:31: #1 tags after filtering in treatment: 9796827 INFO @ Tue, 16 Jun 2020 08:51:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:32: #2 number of paired peaks: 1892 INFO @ Tue, 16 Jun 2020 08:51:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:32: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:51:32: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:51:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.10_model.r INFO @ Tue, 16 Jun 2020 08:51:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.05_summits.bed INFO @ Tue, 16 Jun 2020 08:51:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8496 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:36: 5000000 INFO @ Tue, 16 Jun 2020 08:51:41: 6000000 INFO @ Tue, 16 Jun 2020 08:51:47: 7000000 INFO @ Tue, 16 Jun 2020 08:51:52: 8000000 INFO @ Tue, 16 Jun 2020 08:51:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:57: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:52:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:52:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:52:02: #1 total tags in treatment: 9796827 INFO @ Tue, 16 Jun 2020 08:52:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:02: #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 08:52:02: #1 tags after filtering in treatment: 9796827 INFO @ Tue, 16 Jun 2020 08:52:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:03: #2 number of paired peaks: 1892 INFO @ Tue, 16 Jun 2020 08:52:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:03: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:52:03: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.20_model.r INFO @ Tue, 16 Jun 2020 08:52:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.10_summits.bed INFO @ Tue, 16 Jun 2020 08:52:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5087 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:52:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107865/SRX4107865.20_summits.bed INFO @ Tue, 16 Jun 2020 08:52:36: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2520 records, 4 fields): 4 millis CompletedMACS2peakCalling