Job ID = 6508008 SRX = SRX747301 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:31:03 prefetch.2.10.7: 1) Downloading 'SRR1634999'... 2020-06-26T13:31:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:32:45 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:32:46 prefetch.2.10.7: 'SRR1634999' is valid 2020-06-26T13:32:46 prefetch.2.10.7: 1) 'SRR1634999' was downloaded successfully 2020-06-26T13:33:19 prefetch.2.10.7: 'SRR1634999' has 6 unresolved dependencies 2020-06-26T13:33:19 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-26T13:33:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:33:36 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:33:36 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:33:36 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-26T13:33:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:33:51 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:33:51 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:33:51 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-26T13:33:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:34:07 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:34:07 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:34:07 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-26T13:34:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:34:24 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:34:24 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:34:24 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-26T13:34:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:34:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:34:39 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:34:39 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-26T13:34:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:34:55 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:34:55 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 28914131 spots for SRR1634999/SRR1634999.sra Written 28914131 spots for SRR1634999/SRR1634999.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: 00:03:35 28914131 reads; of these: 28914131 (100.00%) were unpaired; of these: 1262911 (4.37%) aligned 0 times 23596442 (81.61%) aligned exactly 1 time 4054778 (14.02%) aligned >1 times 95.63% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 5377711 / 27651220 = 0.1945 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 @ Fri, 26 Jun 2020 22:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.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 @ Fri, 26 Jun 2020 22:45:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:45:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:45:34: 1000000 INFO @ Fri, 26 Jun 2020 22:45:40: 2000000 INFO @ Fri, 26 Jun 2020 22:45:45: 3000000 INFO @ Fri, 26 Jun 2020 22:45:50: 4000000 INFO @ Fri, 26 Jun 2020 22:45:55: 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 @ Fri, 26 Jun 2020 22:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.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 @ Fri, 26 Jun 2020 22:45:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:45:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:46:01: 6000000 INFO @ Fri, 26 Jun 2020 22:46:05: 1000000 INFO @ Fri, 26 Jun 2020 22:46:07: 7000000 INFO @ Fri, 26 Jun 2020 22:46:11: 2000000 INFO @ Fri, 26 Jun 2020 22:46:12: 8000000 INFO @ Fri, 26 Jun 2020 22:46:17: 3000000 INFO @ Fri, 26 Jun 2020 22:46:18: 9000000 INFO @ Fri, 26 Jun 2020 22:46:23: 4000000 INFO @ Fri, 26 Jun 2020 22:46:24: 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 @ Fri, 26 Jun 2020 22:46:29: 5000000 INFO @ Fri, 26 Jun 2020 22:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.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 @ Fri, 26 Jun 2020 22:46:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:46:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:46:30: 11000000 INFO @ Fri, 26 Jun 2020 22:46:35: 6000000 INFO @ Fri, 26 Jun 2020 22:46:35: 1000000 INFO @ Fri, 26 Jun 2020 22:46:36: 12000000 INFO @ Fri, 26 Jun 2020 22:46:41: 7000000 INFO @ Fri, 26 Jun 2020 22:46:41: 2000000 INFO @ Fri, 26 Jun 2020 22:46:42: 13000000 INFO @ Fri, 26 Jun 2020 22:46:46: 8000000 INFO @ Fri, 26 Jun 2020 22:46:47: 3000000 INFO @ Fri, 26 Jun 2020 22:46:47: 14000000 INFO @ Fri, 26 Jun 2020 22:46:52: 9000000 INFO @ Fri, 26 Jun 2020 22:46:53: 4000000 INFO @ Fri, 26 Jun 2020 22:46:53: 15000000 INFO @ Fri, 26 Jun 2020 22:46:58: 10000000 INFO @ Fri, 26 Jun 2020 22:46:59: 5000000 INFO @ Fri, 26 Jun 2020 22:46:59: 16000000 INFO @ Fri, 26 Jun 2020 22:47:04: 11000000 INFO @ Fri, 26 Jun 2020 22:47:05: 6000000 INFO @ Fri, 26 Jun 2020 22:47:05: 17000000 INFO @ Fri, 26 Jun 2020 22:47:10: 12000000 INFO @ Fri, 26 Jun 2020 22:47:10: 7000000 INFO @ Fri, 26 Jun 2020 22:47:11: 18000000 INFO @ Fri, 26 Jun 2020 22:47:16: 13000000 INFO @ Fri, 26 Jun 2020 22:47:16: 8000000 INFO @ Fri, 26 Jun 2020 22:47:17: 19000000 INFO @ Fri, 26 Jun 2020 22:47:22: 9000000 INFO @ Fri, 26 Jun 2020 22:47:22: 14000000 INFO @ Fri, 26 Jun 2020 22:47:23: 20000000 INFO @ Fri, 26 Jun 2020 22:47:28: 10000000 INFO @ Fri, 26 Jun 2020 22:47:28: 15000000 INFO @ Fri, 26 Jun 2020 22:47:29: 21000000 INFO @ Fri, 26 Jun 2020 22:47:34: 11000000 INFO @ Fri, 26 Jun 2020 22:47:34: 16000000 INFO @ Fri, 26 Jun 2020 22:47:35: 22000000 INFO @ Fri, 26 Jun 2020 22:47:37: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:47:37: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:47:37: #1 total tags in treatment: 22273509 INFO @ Fri, 26 Jun 2020 22:47:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:47:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:47:37: #1 tags after filtering in treatment: 22273509 INFO @ Fri, 26 Jun 2020 22:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:47:37: #1 finished! INFO @ Fri, 26 Jun 2020 22:47:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:47:39: #2 number of paired peaks: 168 WARNING @ Fri, 26 Jun 2020 22:47:39: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 26 Jun 2020 22:47:39: start model_add_line... INFO @ Fri, 26 Jun 2020 22:47:39: start X-correlation... INFO @ Fri, 26 Jun 2020 22:47:39: end of X-cor INFO @ Fri, 26 Jun 2020 22:47:39: #2 finished! INFO @ Fri, 26 Jun 2020 22:47:39: #2 predicted fragment length is 103 bps INFO @ Fri, 26 Jun 2020 22:47:39: #2 alternative fragment length(s) may be 4,103,111 bps INFO @ Fri, 26 Jun 2020 22:47:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.05_model.r INFO @ Fri, 26 Jun 2020 22:47:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:47:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:47:40: 12000000 INFO @ Fri, 26 Jun 2020 22:47:40: 17000000 INFO @ Fri, 26 Jun 2020 22:47:46: 13000000 INFO @ Fri, 26 Jun 2020 22:47:46: 18000000 INFO @ Fri, 26 Jun 2020 22:47:51: 14000000 INFO @ Fri, 26 Jun 2020 22:47:52: 19000000 INFO @ Fri, 26 Jun 2020 22:47:57: 15000000 INFO @ Fri, 26 Jun 2020 22:47:58: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:48:03: 16000000 INFO @ Fri, 26 Jun 2020 22:48:03: 21000000 INFO @ Fri, 26 Jun 2020 22:48:08: 17000000 INFO @ Fri, 26 Jun 2020 22:48:09: 22000000 INFO @ Fri, 26 Jun 2020 22:48:11: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:48:11: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:48:11: #1 total tags in treatment: 22273509 INFO @ Fri, 26 Jun 2020 22:48:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:48:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:48:11: #1 tags after filtering in treatment: 22273509 INFO @ Fri, 26 Jun 2020 22:48:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:48:11: #1 finished! INFO @ Fri, 26 Jun 2020 22:48:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:48:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:48:13: #2 number of paired peaks: 168 WARNING @ Fri, 26 Jun 2020 22:48:13: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 26 Jun 2020 22:48:13: start model_add_line... INFO @ Fri, 26 Jun 2020 22:48:13: start X-correlation... INFO @ Fri, 26 Jun 2020 22:48:13: end of X-cor INFO @ Fri, 26 Jun 2020 22:48:13: #2 finished! INFO @ Fri, 26 Jun 2020 22:48:13: #2 predicted fragment length is 103 bps INFO @ Fri, 26 Jun 2020 22:48:13: #2 alternative fragment length(s) may be 4,103,111 bps INFO @ Fri, 26 Jun 2020 22:48:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.10_model.r INFO @ Fri, 26 Jun 2020 22:48:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:48:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:48:14: 18000000 INFO @ Fri, 26 Jun 2020 22:48:19: 19000000 INFO @ Fri, 26 Jun 2020 22:48:24: 20000000 INFO @ Fri, 26 Jun 2020 22:48:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:48:30: 21000000 INFO @ Fri, 26 Jun 2020 22:48:35: 22000000 INFO @ Fri, 26 Jun 2020 22:48:37: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:48:37: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:48:37: #1 total tags in treatment: 22273509 INFO @ Fri, 26 Jun 2020 22:48:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:48:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:48:37: #1 tags after filtering in treatment: 22273509 INFO @ Fri, 26 Jun 2020 22:48:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:48:37: #1 finished! INFO @ Fri, 26 Jun 2020 22:48:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:48:38: #2 number of paired peaks: 168 WARNING @ Fri, 26 Jun 2020 22:48:38: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 26 Jun 2020 22:48:38: start model_add_line... INFO @ Fri, 26 Jun 2020 22:48:38: start X-correlation... INFO @ Fri, 26 Jun 2020 22:48:38: end of X-cor INFO @ Fri, 26 Jun 2020 22:48:38: #2 finished! INFO @ Fri, 26 Jun 2020 22:48:38: #2 predicted fragment length is 103 bps INFO @ Fri, 26 Jun 2020 22:48:38: #2 alternative fragment length(s) may be 4,103,111 bps INFO @ Fri, 26 Jun 2020 22:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.20_model.r INFO @ Fri, 26 Jun 2020 22:48:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:48:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:48:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:48:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:48:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.05_summits.bed INFO @ Fri, 26 Jun 2020 22:48:48: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (18645 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:48:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:49:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:49:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:49:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.10_summits.bed INFO @ Fri, 26 Jun 2020 22:49:20: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9398 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:49:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:49:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:49:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:49:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747301/SRX747301.20_summits.bed INFO @ Fri, 26 Jun 2020 22:49:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3192 records, 4 fields): 4 millis CompletedMACS2peakCalling