Job ID = 6367893 SRX = SRX4107876 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:45:00 prefetch.2.10.7: 1) Downloading 'SRR7191152'... 2020-06-15T23:45:00 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: 'SRR7191152' is valid 2020-06-15T23:46:06 prefetch.2.10.7: 1) 'SRR7191152' was downloaded successfully 2020-06-15T23:46:39 prefetch.2.10.7: 'SRR7191152' has 6 unresolved dependencies 2020-06-15T23:46:39 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.5?vdb-ctx=refseq'... 2020-06-15T23:46:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:56 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.5?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:46:56 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.5?vdb-ctx=refseq'... 2020-06-15T23:46:56 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: 3) 'ncbi-acc:BX284602.5?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:47:13 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.4?vdb-ctx=refseq'... 2020-06-15T23:47:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:29 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:47:29 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.4?vdb-ctx=refseq'... 2020-06-15T23:47:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:45 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:47:45 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.5?vdb-ctx=refseq'... 2020-06-15T23:47:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:01 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.5?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:48:01 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.5?vdb-ctx=refseq'... 2020-06-15T23:48:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:17 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.5?vdb-ctx=refseq' was downloaded successfully Read 16470012 spots for SRR7191152/SRR7191152.sra Written 16470012 spots for SRR7191152/SRR7191152.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: 00:02:43 16470012 reads; of these: 16470012 (100.00%) were unpaired; of these: 908467 (5.52%) aligned 0 times 13203643 (80.17%) aligned exactly 1 time 2357902 (14.32%) aligned >1 times 94.48% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 2036471 / 15561545 = 0.1309 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 08:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.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 08:55:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:33: 1000000 INFO @ Tue, 16 Jun 2020 08:55:38: 2000000 INFO @ Tue, 16 Jun 2020 08:55:44: 3000000 INFO @ Tue, 16 Jun 2020 08:55:50: 4000000 INFO @ Tue, 16 Jun 2020 08:55:55: 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 08:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.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 08:55:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:01: 6000000 INFO @ Tue, 16 Jun 2020 08:56:04: 1000000 INFO @ Tue, 16 Jun 2020 08:56:08: 7000000 INFO @ Tue, 16 Jun 2020 08:56:10: 2000000 INFO @ Tue, 16 Jun 2020 08:56:15: 8000000 INFO @ Tue, 16 Jun 2020 08:56:17: 3000000 INFO @ Tue, 16 Jun 2020 08:56:21: 9000000 INFO @ Tue, 16 Jun 2020 08:56:24: 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 08:56:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.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 08:56:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:28: 10000000 INFO @ Tue, 16 Jun 2020 08:56:31: 5000000 INFO @ Tue, 16 Jun 2020 08:56:35: 1000000 INFO @ Tue, 16 Jun 2020 08:56:36: 11000000 INFO @ Tue, 16 Jun 2020 08:56:38: 6000000 INFO @ Tue, 16 Jun 2020 08:56:43: 2000000 INFO @ Tue, 16 Jun 2020 08:56:43: 12000000 INFO @ Tue, 16 Jun 2020 08:56:45: 7000000 INFO @ Tue, 16 Jun 2020 08:56:50: 13000000 INFO @ Tue, 16 Jun 2020 08:56:51: 3000000 INFO @ Tue, 16 Jun 2020 08:56:53: 8000000 INFO @ Tue, 16 Jun 2020 08:56:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:54: #1 total tags in treatment: 13525074 INFO @ Tue, 16 Jun 2020 08:56:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:54: #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 08:56:54: #1 tags after filtering in treatment: 13525074 INFO @ Tue, 16 Jun 2020 08:56:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:55: #2 number of paired peaks: 548 WARNING @ Tue, 16 Jun 2020 08:56:55: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:55: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 08:56:55: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 08:56:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.05_model.r INFO @ Tue, 16 Jun 2020 08:56:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:58: 4000000 INFO @ Tue, 16 Jun 2020 08:57:00: 9000000 INFO @ Tue, 16 Jun 2020 08:57:06: 5000000 INFO @ Tue, 16 Jun 2020 08:57:07: 10000000 INFO @ Tue, 16 Jun 2020 08:57:14: 6000000 INFO @ Tue, 16 Jun 2020 08:57:14: 11000000 INFO @ Tue, 16 Jun 2020 08:57:21: 12000000 INFO @ Tue, 16 Jun 2020 08:57:22: 7000000 INFO @ Tue, 16 Jun 2020 08:57:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:28: 13000000 INFO @ Tue, 16 Jun 2020 08:57:30: 8000000 INFO @ Tue, 16 Jun 2020 08:57:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:32: #1 total tags in treatment: 13525074 INFO @ Tue, 16 Jun 2020 08:57:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:32: #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 08:57:32: #1 tags after filtering in treatment: 13525074 INFO @ Tue, 16 Jun 2020 08:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:33: #2 number of paired peaks: 548 WARNING @ Tue, 16 Jun 2020 08:57:33: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:33: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 08:57:33: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 08:57:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.10_model.r INFO @ Tue, 16 Jun 2020 08:57:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:33: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:57:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5233 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:37: 9000000 INFO @ Tue, 16 Jun 2020 08:57:44: 10000000 INFO @ Tue, 16 Jun 2020 08:57:51: 11000000 INFO @ Tue, 16 Jun 2020 08:57:58: 12000000 INFO @ Tue, 16 Jun 2020 08:58:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:58:05: 13000000 INFO @ Tue, 16 Jun 2020 08:58:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:58:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:58:09: #1 total tags in treatment: 13525074 INFO @ Tue, 16 Jun 2020 08:58:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:09: #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 08:58:09: #1 tags after filtering in treatment: 13525074 INFO @ Tue, 16 Jun 2020 08:58:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:10: #2 number of paired peaks: 548 WARNING @ Tue, 16 Jun 2020 08:58:10: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:10: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 08:58:10: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 08:58:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.20_model.r INFO @ Tue, 16 Jun 2020 08:58:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3610 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4107876/SRX4107876.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2102 records, 4 fields): 3 millis CompletedMACS2peakCalling