Job ID = 6367680 SRX = SRX3883435 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:35 prefetch.2.10.7: 1) Downloading 'SRR6938930'... 2020-06-15T23:32:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:34 prefetch.2.10.7: 'SRR6938930' is valid 2020-06-15T23:35:34 prefetch.2.10.7: 1) 'SRR6938930' was downloaded successfully 2020-06-15T23:35:34 prefetch.2.10.7: 'SRR6938930' has 0 unresolved dependencies Read 22331954 spots for SRR6938930/SRR6938930.sra Written 22331954 spots for SRR6938930/SRR6938930.sra 2020-06-15T23:36:57 prefetch.2.10.7: 1) Downloading 'SRR6938931'... 2020-06-15T23:36:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:48 prefetch.2.10.7: 'SRR6938931' is valid 2020-06-15T23:38:48 prefetch.2.10.7: 1) 'SRR6938931' was downloaded successfully 2020-06-15T23:38:48 prefetch.2.10.7: 'SRR6938931' has 0 unresolved dependencies Read 15421996 spots for SRR6938931/SRR6938931.sra Written 15421996 spots for SRR6938931/SRR6938931.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: 00:07:11 37753950 reads; of these: 37753950 (100.00%) were unpaired; of these: 8989428 (23.81%) aligned 0 times 23987734 (63.54%) aligned exactly 1 time 4776788 (12.65%) aligned >1 times 76.19% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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 12 files... [bam_rmdupse_core] 4178223 / 28764522 = 0.1453 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 08:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.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 08:53:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:25: 1000000 INFO @ Tue, 16 Jun 2020 08:53:31: 2000000 INFO @ Tue, 16 Jun 2020 08:53:37: 3000000 INFO @ Tue, 16 Jun 2020 08:53:43: 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 08:53:49: 5000000 INFO @ Tue, 16 Jun 2020 08:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.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 08:53:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:56: 6000000 INFO @ Tue, 16 Jun 2020 08:53:56: 1000000 INFO @ Tue, 16 Jun 2020 08:54:02: 7000000 INFO @ Tue, 16 Jun 2020 08:54:02: 2000000 INFO @ Tue, 16 Jun 2020 08:54:08: 8000000 INFO @ Tue, 16 Jun 2020 08:54:08: 3000000 INFO @ Tue, 16 Jun 2020 08:54:14: 9000000 INFO @ Tue, 16 Jun 2020 08:54:15: 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 08:54:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.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 08:54:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:20: 10000000 INFO @ Tue, 16 Jun 2020 08:54:21: 5000000 INFO @ Tue, 16 Jun 2020 08:54:26: 1000000 INFO @ Tue, 16 Jun 2020 08:54:27: 11000000 INFO @ Tue, 16 Jun 2020 08:54:27: 6000000 INFO @ Tue, 16 Jun 2020 08:54:33: 2000000 INFO @ Tue, 16 Jun 2020 08:54:33: 12000000 INFO @ Tue, 16 Jun 2020 08:54:34: 7000000 INFO @ Tue, 16 Jun 2020 08:54:39: 13000000 INFO @ Tue, 16 Jun 2020 08:54:39: 3000000 INFO @ Tue, 16 Jun 2020 08:54:40: 8000000 INFO @ Tue, 16 Jun 2020 08:54:45: 14000000 INFO @ Tue, 16 Jun 2020 08:54:45: 4000000 INFO @ Tue, 16 Jun 2020 08:54:47: 9000000 INFO @ Tue, 16 Jun 2020 08:54:51: 15000000 INFO @ Tue, 16 Jun 2020 08:54:51: 5000000 INFO @ Tue, 16 Jun 2020 08:54:53: 10000000 INFO @ Tue, 16 Jun 2020 08:54:57: 16000000 INFO @ Tue, 16 Jun 2020 08:54:58: 6000000 INFO @ Tue, 16 Jun 2020 08:54:59: 11000000 INFO @ Tue, 16 Jun 2020 08:55:03: 17000000 INFO @ Tue, 16 Jun 2020 08:55:04: 7000000 INFO @ Tue, 16 Jun 2020 08:55:05: 12000000 INFO @ Tue, 16 Jun 2020 08:55:09: 18000000 INFO @ Tue, 16 Jun 2020 08:55:10: 8000000 INFO @ Tue, 16 Jun 2020 08:55:11: 13000000 INFO @ Tue, 16 Jun 2020 08:55:16: 19000000 INFO @ Tue, 16 Jun 2020 08:55:16: 9000000 INFO @ Tue, 16 Jun 2020 08:55:17: 14000000 INFO @ Tue, 16 Jun 2020 08:55:22: 20000000 INFO @ Tue, 16 Jun 2020 08:55:22: 10000000 INFO @ Tue, 16 Jun 2020 08:55:24: 15000000 INFO @ Tue, 16 Jun 2020 08:55:28: 21000000 INFO @ Tue, 16 Jun 2020 08:55:28: 11000000 INFO @ Tue, 16 Jun 2020 08:55:30: 16000000 INFO @ Tue, 16 Jun 2020 08:55:34: 22000000 INFO @ Tue, 16 Jun 2020 08:55:35: 12000000 INFO @ Tue, 16 Jun 2020 08:55:36: 17000000 INFO @ Tue, 16 Jun 2020 08:55:40: 23000000 INFO @ Tue, 16 Jun 2020 08:55:41: 13000000 INFO @ Tue, 16 Jun 2020 08:55:42: 18000000 INFO @ Tue, 16 Jun 2020 08:55:45: 24000000 INFO @ Tue, 16 Jun 2020 08:55:47: 14000000 INFO @ Tue, 16 Jun 2020 08:55:48: 19000000 INFO @ Tue, 16 Jun 2020 08:55:49: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:55:49: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:55:49: #1 total tags in treatment: 24586299 INFO @ Tue, 16 Jun 2020 08:55:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:49: #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 08:55:49: #1 tags after filtering in treatment: 24586299 INFO @ Tue, 16 Jun 2020 08:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:51: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 08:55:51: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:51: #2 predicted fragment length is 173 bps INFO @ Tue, 16 Jun 2020 08:55:51: #2 alternative fragment length(s) may be 2,173 bps INFO @ Tue, 16 Jun 2020 08:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.05_model.r INFO @ Tue, 16 Jun 2020 08:55:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:53: 15000000 INFO @ Tue, 16 Jun 2020 08:55:54: 20000000 INFO @ Tue, 16 Jun 2020 08:55:59: 16000000 INFO @ Tue, 16 Jun 2020 08:56:00: 21000000 INFO @ Tue, 16 Jun 2020 08:56:05: 17000000 INFO @ Tue, 16 Jun 2020 08:56:06: 22000000 INFO @ Tue, 16 Jun 2020 08:56:11: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:56:12: 23000000 INFO @ Tue, 16 Jun 2020 08:56:16: 19000000 INFO @ Tue, 16 Jun 2020 08:56:17: 24000000 INFO @ Tue, 16 Jun 2020 08:56:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:21: #1 total tags in treatment: 24586299 INFO @ Tue, 16 Jun 2020 08:56:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:21: #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 08:56:21: #1 tags after filtering in treatment: 24586299 INFO @ Tue, 16 Jun 2020 08:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:22: 20000000 INFO @ Tue, 16 Jun 2020 08:56:23: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 08:56:23: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:23: #2 predicted fragment length is 173 bps INFO @ Tue, 16 Jun 2020 08:56:23: #2 alternative fragment length(s) may be 2,173 bps INFO @ Tue, 16 Jun 2020 08:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.10_model.r INFO @ Tue, 16 Jun 2020 08:56:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:28: 21000000 INFO @ Tue, 16 Jun 2020 08:56:34: 22000000 INFO @ Tue, 16 Jun 2020 08:56:40: 23000000 INFO @ Tue, 16 Jun 2020 08:56:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:45: 24000000 INFO @ Tue, 16 Jun 2020 08:56:49: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:49: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:49: #1 total tags in treatment: 24586299 INFO @ Tue, 16 Jun 2020 08:56:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:49: #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 08:56:49: #1 tags after filtering in treatment: 24586299 INFO @ Tue, 16 Jun 2020 08:56:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:51: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 08:56:51: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:51: #2 predicted fragment length is 173 bps INFO @ Tue, 16 Jun 2020 08:56:51: #2 alternative fragment length(s) may be 2,173 bps INFO @ Tue, 16 Jun 2020 08:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.20_model.r INFO @ Tue, 16 Jun 2020 08:56:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1881 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:57:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.10_summits.bed INFO @ Tue, 16 Jun 2020 08:57:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (835 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3883435/SRX3883435.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 1 millis CompletedMACS2peakCalling