Job ID = 6367020 SRX = SRX2710281 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:16:16 prefetch.2.10.7: 1) Downloading 'SRR5418735'... 2020-06-15T23:16:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:42 prefetch.2.10.7: 1) 'SRR5418735' was downloaded successfully Read 63135631 spots for SRR5418735/SRR5418735.sra Written 63135631 spots for SRR5418735/SRR5418735.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: 00:18:23 63135631 reads; of these: 63135631 (100.00%) were unpaired; of these: 6481499 (10.27%) aligned 0 times 24284163 (38.46%) aligned exactly 1 time 32369969 (51.27%) aligned >1 times 89.73% overall alignment rate Time searching: 00:18:23 Overall time: 00:18:23 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 24 files... [bam_rmdupse_core] 39752450 / 56654132 = 0.7017 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 08:53:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.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 08:53:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:37: 1000000 INFO @ Tue, 16 Jun 2020 08:53:44: 2000000 INFO @ Tue, 16 Jun 2020 08:53:51: 3000000 INFO @ Tue, 16 Jun 2020 08:53:58: 4000000 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 08:54:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.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 08:54:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:05: 5000000 INFO @ Tue, 16 Jun 2020 08:54:08: 1000000 INFO @ Tue, 16 Jun 2020 08:54:12: 6000000 INFO @ Tue, 16 Jun 2020 08:54:15: 2000000 INFO @ Tue, 16 Jun 2020 08:54:19: 7000000 INFO @ Tue, 16 Jun 2020 08:54:22: 3000000 INFO @ Tue, 16 Jun 2020 08:54:26: 8000000 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 08:54:29: 4000000 INFO @ Tue, 16 Jun 2020 08:54:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.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 08:54:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:34: 9000000 INFO @ Tue, 16 Jun 2020 08:54:36: 5000000 INFO @ Tue, 16 Jun 2020 08:54:38: 1000000 INFO @ Tue, 16 Jun 2020 08:54:41: 10000000 INFO @ Tue, 16 Jun 2020 08:54:43: 6000000 INFO @ Tue, 16 Jun 2020 08:54:45: 2000000 INFO @ Tue, 16 Jun 2020 08:54:48: 11000000 INFO @ Tue, 16 Jun 2020 08:54:50: 7000000 INFO @ Tue, 16 Jun 2020 08:54:52: 3000000 INFO @ Tue, 16 Jun 2020 08:54:56: 12000000 INFO @ Tue, 16 Jun 2020 08:54:58: 8000000 INFO @ Tue, 16 Jun 2020 08:55:00: 4000000 INFO @ Tue, 16 Jun 2020 08:55:03: 13000000 INFO @ Tue, 16 Jun 2020 08:55:05: 9000000 INFO @ Tue, 16 Jun 2020 08:55:07: 5000000 INFO @ Tue, 16 Jun 2020 08:55:11: 14000000 INFO @ Tue, 16 Jun 2020 08:55:12: 10000000 INFO @ Tue, 16 Jun 2020 08:55:14: 6000000 INFO @ Tue, 16 Jun 2020 08:55:18: 15000000 INFO @ Tue, 16 Jun 2020 08:55:20: 11000000 INFO @ Tue, 16 Jun 2020 08:55:21: 7000000 INFO @ Tue, 16 Jun 2020 08:55:25: 16000000 INFO @ Tue, 16 Jun 2020 08:55:27: 12000000 INFO @ Tue, 16 Jun 2020 08:55:29: 8000000 INFO @ Tue, 16 Jun 2020 08:55:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:55:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:55:32: #1 total tags in treatment: 16901682 INFO @ Tue, 16 Jun 2020 08:55:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:32: #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 08:55:32: #1 tags after filtering in treatment: 16901682 INFO @ Tue, 16 Jun 2020 08:55:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:34: #2 number of paired peaks: 1395 INFO @ Tue, 16 Jun 2020 08:55:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:34: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:55:34: #2 alternative fragment length(s) may be 4,106 bps INFO @ Tue, 16 Jun 2020 08:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.05_model.r INFO @ Tue, 16 Jun 2020 08:55:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:34: 13000000 INFO @ Tue, 16 Jun 2020 08:55:36: 9000000 INFO @ Tue, 16 Jun 2020 08:55:42: 14000000 INFO @ Tue, 16 Jun 2020 08:55:44: 10000000 INFO @ Tue, 16 Jun 2020 08:55:49: 15000000 INFO @ Tue, 16 Jun 2020 08:55:51: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:55:56: 16000000 INFO @ Tue, 16 Jun 2020 08:55:58: 12000000 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: 16901682 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: 16901682 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 08:56:04: #2 number of paired peaks: 1395 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 106 bps INFO @ Tue, 16 Jun 2020 08:56:04: #2 alternative fragment length(s) may be 4,106 bps INFO @ Tue, 16 Jun 2020 08:56:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.10_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 08:56:06: 13000000 INFO @ Tue, 16 Jun 2020 08:56:13: 14000000 INFO @ Tue, 16 Jun 2020 08:56:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:20: 15000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:56:27: 16000000 INFO @ Tue, 16 Jun 2020 08:56:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:33: #1 total tags in treatment: 16901682 INFO @ Tue, 16 Jun 2020 08:56:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:33: #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 08:56:33: #1 tags after filtering in treatment: 16901682 INFO @ Tue, 16 Jun 2020 08:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.05_summits.bed INFO @ Tue, 16 Jun 2020 08:56:34: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (24527 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:35: #2 number of paired peaks: 1395 INFO @ Tue, 16 Jun 2020 08:56:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:35: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:56:35: #2 alternative fragment length(s) may be 4,106 bps INFO @ Tue, 16 Jun 2020 08:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.20_model.r INFO @ Tue, 16 Jun 2020 08:56:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.10_summits.bed INFO @ Tue, 16 Jun 2020 08:57:03: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (16424 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710281/SRX2710281.20_summits.bed INFO @ Tue, 16 Jun 2020 08:57:35: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (9108 records, 4 fields): 12 millis CompletedMACS2peakCalling