Job ID = 6366732 SRX = SRX2228885 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:59 prefetch.2.10.7: 1) Downloading 'SRR4380341'... 2020-06-15T22:54:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:43 prefetch.2.10.7: 'SRR4380341' is valid 2020-06-15T22:56:43 prefetch.2.10.7: 1) 'SRR4380341' was downloaded successfully 2020-06-15T22:56:43 prefetch.2.10.7: 'SRR4380341' has 0 unresolved dependencies Read 20205412 spots for SRR4380341/SRR4380341.sra Written 20205412 spots for SRR4380341/SRR4380341.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: 00:04:17 20205412 reads; of these: 20205412 (100.00%) were unpaired; of these: 2660964 (13.17%) aligned 0 times 14705532 (72.78%) aligned exactly 1 time 2838916 (14.05%) aligned >1 times 86.83% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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] 3163644 / 17544448 = 0.1803 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 08:06:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.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 08:06:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:12: 1000000 INFO @ Tue, 16 Jun 2020 08:06:17: 2000000 INFO @ Tue, 16 Jun 2020 08:06:22: 3000000 INFO @ Tue, 16 Jun 2020 08:06:27: 4000000 INFO @ Tue, 16 Jun 2020 08:06:32: 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 08:06:37: 6000000 INFO @ Tue, 16 Jun 2020 08:06:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.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 08:06:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:42: 7000000 INFO @ Tue, 16 Jun 2020 08:06:42: 1000000 INFO @ Tue, 16 Jun 2020 08:06:47: 8000000 INFO @ Tue, 16 Jun 2020 08:06:47: 2000000 INFO @ Tue, 16 Jun 2020 08:06:52: 9000000 INFO @ Tue, 16 Jun 2020 08:06:53: 3000000 INFO @ Tue, 16 Jun 2020 08:06:57: 10000000 INFO @ Tue, 16 Jun 2020 08:06:58: 4000000 INFO @ Tue, 16 Jun 2020 08:07:02: 11000000 INFO @ Tue, 16 Jun 2020 08:07:03: 5000000 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 08:07:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.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 08:07:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:07: 12000000 INFO @ Tue, 16 Jun 2020 08:07:08: 6000000 INFO @ Tue, 16 Jun 2020 08:07:12: 13000000 INFO @ Tue, 16 Jun 2020 08:07:13: 1000000 INFO @ Tue, 16 Jun 2020 08:07:13: 7000000 INFO @ Tue, 16 Jun 2020 08:07:17: 14000000 INFO @ Tue, 16 Jun 2020 08:07:18: 8000000 INFO @ Tue, 16 Jun 2020 08:07:19: 2000000 INFO @ Tue, 16 Jun 2020 08:07:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:19: #1 total tags in treatment: 14380804 INFO @ Tue, 16 Jun 2020 08:07:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:19: #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 08:07:20: #1 tags after filtering in treatment: 14380804 INFO @ Tue, 16 Jun 2020 08:07:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:20: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 08:07:20: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:21: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:07:21: #2 alternative fragment length(s) may be 4,110 bps INFO @ Tue, 16 Jun 2020 08:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.05_model.r INFO @ Tue, 16 Jun 2020 08:07:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:24: 9000000 INFO @ Tue, 16 Jun 2020 08:07:24: 3000000 INFO @ Tue, 16 Jun 2020 08:07:29: 10000000 INFO @ Tue, 16 Jun 2020 08:07:30: 4000000 INFO @ Tue, 16 Jun 2020 08:07:34: 11000000 INFO @ Tue, 16 Jun 2020 08:07:36: 5000000 INFO @ Tue, 16 Jun 2020 08:07:40: 12000000 INFO @ Tue, 16 Jun 2020 08:07:42: 6000000 INFO @ Tue, 16 Jun 2020 08:07:45: 13000000 INFO @ Tue, 16 Jun 2020 08:07:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:48: 7000000 INFO @ Tue, 16 Jun 2020 08:07:50: 14000000 INFO @ Tue, 16 Jun 2020 08:07:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:52: #1 total tags in treatment: 14380804 INFO @ Tue, 16 Jun 2020 08:07:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:52: #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 08:07:52: #1 tags after filtering in treatment: 14380804 INFO @ Tue, 16 Jun 2020 08:07:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:53: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 08:07:53: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:53: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:07:53: #2 alternative fragment length(s) may be 4,110 bps INFO @ Tue, 16 Jun 2020 08:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.10_model.r INFO @ Tue, 16 Jun 2020 08:07:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:53: 8000000 INFO @ Tue, 16 Jun 2020 08:07:59: 9000000 INFO @ Tue, 16 Jun 2020 08:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1732 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:05: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:10: 11000000 INFO @ Tue, 16 Jun 2020 08:08:16: 12000000 INFO @ Tue, 16 Jun 2020 08:08:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:21: 13000000 INFO @ Tue, 16 Jun 2020 08:08:27: 14000000 INFO @ Tue, 16 Jun 2020 08:08:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:08:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:08:29: #1 total tags in treatment: 14380804 INFO @ Tue, 16 Jun 2020 08:08:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:29: #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 08:08:29: #1 tags after filtering in treatment: 14380804 INFO @ Tue, 16 Jun 2020 08:08:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:30: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 08:08:30: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:30: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:08:30: #2 alternative fragment length(s) may be 4,110 bps INFO @ Tue, 16 Jun 2020 08:08:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.20_model.r INFO @ Tue, 16 Jun 2020 08:08:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1100 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:08:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228885/SRX2228885.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (629 records, 4 fields): 11 millis CompletedMACS2peakCalling