Job ID = 6367894 SRX = SRX4107877 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:43:44 prefetch.2.10.7: 1) Downloading 'SRR7191153'... 2020-06-15T23:43:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:17 prefetch.2.10.7: 'SRR7191153' is valid 2020-06-15T23:45:17 prefetch.2.10.7: 1) 'SRR7191153' was downloaded successfully 2020-06-15T23:45:50 prefetch.2.10.7: 'SRR7191153' has 6 unresolved dependencies 2020-06-15T23:45:50 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.5?vdb-ctx=refseq'... 2020-06-15T23:45:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:06 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.5?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:46:06 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.5?vdb-ctx=refseq'... 2020-06-15T23:46:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:23 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.5?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:46:23 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.4?vdb-ctx=refseq'... 2020-06-15T23:46:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:39 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:39 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:46:39 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.4?vdb-ctx=refseq'... 2020-06-15T23:46:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:57 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:46:57 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.5?vdb-ctx=refseq'... 2020-06-15T23:46:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:13 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.5?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:47:13 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.5?vdb-ctx=refseq'... 2020-06-15T23:47:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:31 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.5?vdb-ctx=refseq' was downloaded successfully Read 16364174 spots for SRR7191153/SRR7191153.sra Written 16364174 spots for SRR7191153/SRR7191153.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 16364174 reads; of these: 16364174 (100.00%) were unpaired; of these: 1050848 (6.42%) aligned 0 times 12998241 (79.43%) aligned exactly 1 time 2315085 (14.15%) aligned >1 times 93.58% 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] 1899623 / 15313326 = 0.1241 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 08:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.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 08:54:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:52: 1000000 INFO @ Tue, 16 Jun 2020 08:54:57: 2000000 INFO @ Tue, 16 Jun 2020 08:55:02: 3000000 INFO @ Tue, 16 Jun 2020 08:55:08: 4000000 INFO @ Tue, 16 Jun 2020 08:55:13: 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 08:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.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 08:55:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:19: 6000000 INFO @ Tue, 16 Jun 2020 08:55:22: 1000000 INFO @ Tue, 16 Jun 2020 08:55:25: 7000000 INFO @ Tue, 16 Jun 2020 08:55:28: 2000000 INFO @ Tue, 16 Jun 2020 08:55:30: 8000000 INFO @ Tue, 16 Jun 2020 08:55:34: 3000000 INFO @ Tue, 16 Jun 2020 08:55:36: 9000000 INFO @ Tue, 16 Jun 2020 08:55:40: 4000000 INFO @ Tue, 16 Jun 2020 08:55:42: 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 08:55:45: 5000000 INFO @ Tue, 16 Jun 2020 08:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.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 08:55:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:48: 11000000 INFO @ Tue, 16 Jun 2020 08:55:51: 6000000 INFO @ Tue, 16 Jun 2020 08:55:53: 1000000 INFO @ Tue, 16 Jun 2020 08:55:54: 12000000 INFO @ Tue, 16 Jun 2020 08:55:57: 7000000 INFO @ Tue, 16 Jun 2020 08:56:00: 13000000 INFO @ Tue, 16 Jun 2020 08:56:00: 2000000 INFO @ Tue, 16 Jun 2020 08:56:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:02: #1 total tags in treatment: 13413703 INFO @ Tue, 16 Jun 2020 08:56:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:02: #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 08:56:03: #1 tags after filtering in treatment: 13413703 INFO @ Tue, 16 Jun 2020 08:56:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:03: 8000000 INFO @ Tue, 16 Jun 2020 08:56:04: #2 number of paired peaks: 466 WARNING @ Tue, 16 Jun 2020 08:56:04: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:04: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 08:56:04: #2 alternative fragment length(s) may be 118 bps INFO @ Tue, 16 Jun 2020 08:56:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.05_model.r INFO @ Tue, 16 Jun 2020 08:56:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:07: 3000000 INFO @ Tue, 16 Jun 2020 08:56:10: 9000000 INFO @ Tue, 16 Jun 2020 08:56:14: 4000000 INFO @ Tue, 16 Jun 2020 08:56:16: 10000000 INFO @ Tue, 16 Jun 2020 08:56:21: 5000000 INFO @ Tue, 16 Jun 2020 08:56:22: 11000000 INFO @ Tue, 16 Jun 2020 08:56:28: 6000000 INFO @ Tue, 16 Jun 2020 08:56:28: 12000000 INFO @ Tue, 16 Jun 2020 08:56:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:35: 13000000 INFO @ Tue, 16 Jun 2020 08:56:35: 7000000 INFO @ Tue, 16 Jun 2020 08:56:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:37: #1 total tags in treatment: 13413703 INFO @ Tue, 16 Jun 2020 08:56:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:37: #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 08:56:37: #1 tags after filtering in treatment: 13413703 INFO @ Tue, 16 Jun 2020 08:56:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:38: #2 number of paired peaks: 466 WARNING @ Tue, 16 Jun 2020 08:56:38: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:39: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 08:56:39: #2 alternative fragment length(s) may be 118 bps INFO @ Tue, 16 Jun 2020 08:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.10_model.r INFO @ Tue, 16 Jun 2020 08:56:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:41: 8000000 INFO @ Tue, 16 Jun 2020 08:56:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.05_summits.bed INFO @ Tue, 16 Jun 2020 08:56:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5016 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:48: 9000000 INFO @ Tue, 16 Jun 2020 08:56:54: 10000000 INFO @ Tue, 16 Jun 2020 08:57:01: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:57:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:07: 12000000 INFO @ Tue, 16 Jun 2020 08:57:14: 13000000 INFO @ Tue, 16 Jun 2020 08:57:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:16: #1 total tags in treatment: 13413703 INFO @ Tue, 16 Jun 2020 08:57:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:16: #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 08:57:17: #1 tags after filtering in treatment: 13413703 INFO @ Tue, 16 Jun 2020 08:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:18: #2 number of paired peaks: 466 WARNING @ Tue, 16 Jun 2020 08:57:18: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:18: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 08:57:18: #2 alternative fragment length(s) may be 118 bps INFO @ Tue, 16 Jun 2020 08:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.20_model.r INFO @ Tue, 16 Jun 2020 08:57:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.10_summits.bed INFO @ Tue, 16 Jun 2020 08:57:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3523 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:57:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107877/SRX4107877.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1970 records, 4 fields): 4 millis CompletedMACS2peakCalling