Job ID = 6367661 SRX = SRX3733155 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:41:29 prefetch.2.10.7: 1) Downloading 'SRR6760668'... 2020-06-15T23:41:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:40 prefetch.2.10.7: 1) 'SRR6760668' was downloaded successfully 2020-06-15T23:49:40 prefetch.2.10.7: 'SRR6760668' has 0 unresolved dependencies Read 23736589 spots for SRR6760668/SRR6760668.sra Written 23736589 spots for SRR6760668/SRR6760668.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: 00:30:49 23736589 reads; of these: 23736589 (100.00%) were paired; of these: 3026972 (12.75%) aligned concordantly 0 times 18390614 (77.48%) aligned concordantly exactly 1 time 2319003 (9.77%) aligned concordantly >1 times ---- 3026972 pairs aligned concordantly 0 times; of these: 581988 (19.23%) aligned discordantly 1 time ---- 2444984 pairs aligned 0 times concordantly or discordantly; of these: 4889968 mates make up the pairs; of these: 4186757 (85.62%) aligned 0 times 449401 (9.19%) aligned exactly 1 time 253810 (5.19%) aligned >1 times 91.18% overall alignment rate Time searching: 00:30:49 Overall time: 00:30:49 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 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 14480532 / 21261532 = 0.6811 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 09:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.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 09:33:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:48: 1000000 INFO @ Tue, 16 Jun 2020 09:33:57: 2000000 INFO @ Tue, 16 Jun 2020 09:34:05: 3000000 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 09:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.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 09:34:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:13: 4000000 INFO @ Tue, 16 Jun 2020 09:34:18: 1000000 INFO @ Tue, 16 Jun 2020 09:34:22: 5000000 INFO @ Tue, 16 Jun 2020 09:34:26: 2000000 INFO @ Tue, 16 Jun 2020 09:34:31: 6000000 INFO @ Tue, 16 Jun 2020 09:34:34: 3000000 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 09:34:39: 7000000 INFO @ Tue, 16 Jun 2020 09:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.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 09:34:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:43: 4000000 INFO @ Tue, 16 Jun 2020 09:34:48: 1000000 INFO @ Tue, 16 Jun 2020 09:34:48: 8000000 INFO @ Tue, 16 Jun 2020 09:34:51: 5000000 INFO @ Tue, 16 Jun 2020 09:34:57: 2000000 INFO @ Tue, 16 Jun 2020 09:34:57: 9000000 INFO @ Tue, 16 Jun 2020 09:35:00: 6000000 INFO @ Tue, 16 Jun 2020 09:35:05: 3000000 INFO @ Tue, 16 Jun 2020 09:35:07: 10000000 INFO @ Tue, 16 Jun 2020 09:35:08: 7000000 INFO @ Tue, 16 Jun 2020 09:35:13: 4000000 INFO @ Tue, 16 Jun 2020 09:35:16: 11000000 INFO @ Tue, 16 Jun 2020 09:35:16: 8000000 INFO @ Tue, 16 Jun 2020 09:35:22: 5000000 INFO @ Tue, 16 Jun 2020 09:35:24: 12000000 INFO @ Tue, 16 Jun 2020 09:35:25: 9000000 INFO @ Tue, 16 Jun 2020 09:35:30: 6000000 INFO @ Tue, 16 Jun 2020 09:35:33: 10000000 INFO @ Tue, 16 Jun 2020 09:35:33: 13000000 INFO @ Tue, 16 Jun 2020 09:35:39: 7000000 INFO @ Tue, 16 Jun 2020 09:35:41: 11000000 INFO @ Tue, 16 Jun 2020 09:35:43: 14000000 INFO @ Tue, 16 Jun 2020 09:35:46: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:35:46: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:35:46: #1 total tags in treatment: 6510265 INFO @ Tue, 16 Jun 2020 09:35:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:46: #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 09:35:46: #1 tags after filtering in treatment: 5329299 INFO @ Tue, 16 Jun 2020 09:35:46: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 16 Jun 2020 09:35:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:46: #2 number of paired peaks: 642 WARNING @ Tue, 16 Jun 2020 09:35:46: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:46: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 09:35:46: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 16 Jun 2020 09:35:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.05_model.r INFO @ Tue, 16 Jun 2020 09:35:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:47: 8000000 INFO @ Tue, 16 Jun 2020 09:35:49: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:55: 9000000 INFO @ Tue, 16 Jun 2020 09:35:57: 13000000 INFO @ Tue, 16 Jun 2020 09:35:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:03: 10000000 INFO @ Tue, 16 Jun 2020 09:36:05: 14000000 INFO @ Tue, 16 Jun 2020 09:36:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (499 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:07: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:36:07: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:36:07: #1 total tags in treatment: 6510265 INFO @ Tue, 16 Jun 2020 09:36:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:07: #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 09:36:08: #1 tags after filtering in treatment: 5329299 INFO @ Tue, 16 Jun 2020 09:36:08: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 16 Jun 2020 09:36:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:08: #2 number of paired peaks: 642 WARNING @ Tue, 16 Jun 2020 09:36:08: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:08: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 09:36:08: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 16 Jun 2020 09:36:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.10_model.r INFO @ Tue, 16 Jun 2020 09:36:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:10: 11000000 INFO @ Tue, 16 Jun 2020 09:36:18: 12000000 INFO @ Tue, 16 Jun 2020 09:36:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:25: 13000000 INFO @ Tue, 16 Jun 2020 09:36:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (352 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:32: 14000000 INFO @ Tue, 16 Jun 2020 09:36:34: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:36:34: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:36:34: #1 total tags in treatment: 6510265 INFO @ Tue, 16 Jun 2020 09:36:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:34: #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 09:36:34: #1 tags after filtering in treatment: 5329299 INFO @ Tue, 16 Jun 2020 09:36:34: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 16 Jun 2020 09:36:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:35: #2 number of paired peaks: 642 WARNING @ Tue, 16 Jun 2020 09:36:35: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:35: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 09:36:35: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 16 Jun 2020 09:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.20_model.r INFO @ Tue, 16 Jun 2020 09:36:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733155/SRX3733155.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (225 records, 4 fields): 1 millis CompletedMACS2peakCalling