Job ID = 6366651 SRX = SRX2163952 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:16:31 prefetch.2.10.7: 1) Downloading 'SRR4242867'... 2020-06-15T23:16:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:26:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:26:22 prefetch.2.10.7: 1) 'SRR4242867' was downloaded successfully Read 70355128 spots for SRR4242867/SRR4242867.sra Written 70355128 spots for SRR4242867/SRR4242867.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: 00:23:04 70355128 reads; of these: 70355128 (100.00%) were unpaired; of these: 20848525 (29.63%) aligned 0 times 41548885 (59.06%) aligned exactly 1 time 7957718 (11.31%) aligned >1 times 70.37% overall alignment rate Time searching: 00:23:04 Overall time: 00:23:04 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] 26579918 / 49506603 = 0.5369 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 09:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.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 09:09:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:57: 1000000 INFO @ Tue, 16 Jun 2020 09:10:07: 2000000 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 09:10:16: 3000000 INFO @ Tue, 16 Jun 2020 09:10:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.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 09:10:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:26: 1000000 INFO @ Tue, 16 Jun 2020 09:10:27: 4000000 INFO @ Tue, 16 Jun 2020 09:10:35: 2000000 INFO @ Tue, 16 Jun 2020 09:10:37: 5000000 INFO @ Tue, 16 Jun 2020 09:10:44: 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 09:10:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.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 09:10:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:48: 6000000 INFO @ Tue, 16 Jun 2020 09:10:54: 4000000 INFO @ Tue, 16 Jun 2020 09:10:57: 1000000 INFO @ Tue, 16 Jun 2020 09:10:58: 7000000 INFO @ Tue, 16 Jun 2020 09:11:04: 5000000 INFO @ Tue, 16 Jun 2020 09:11:06: 2000000 INFO @ Tue, 16 Jun 2020 09:11:08: 8000000 INFO @ Tue, 16 Jun 2020 09:11:13: 6000000 INFO @ Tue, 16 Jun 2020 09:11:16: 3000000 INFO @ Tue, 16 Jun 2020 09:11:19: 9000000 INFO @ Tue, 16 Jun 2020 09:11:23: 7000000 INFO @ Tue, 16 Jun 2020 09:11:26: 4000000 INFO @ Tue, 16 Jun 2020 09:11:29: 10000000 INFO @ Tue, 16 Jun 2020 09:11:32: 8000000 INFO @ Tue, 16 Jun 2020 09:11:35: 5000000 INFO @ Tue, 16 Jun 2020 09:11:40: 11000000 INFO @ Tue, 16 Jun 2020 09:11:42: 9000000 INFO @ Tue, 16 Jun 2020 09:11:45: 6000000 INFO @ Tue, 16 Jun 2020 09:11:50: 12000000 INFO @ Tue, 16 Jun 2020 09:11:52: 10000000 INFO @ Tue, 16 Jun 2020 09:11:54: 7000000 INFO @ Tue, 16 Jun 2020 09:12:00: 13000000 INFO @ Tue, 16 Jun 2020 09:12:01: 11000000 INFO @ Tue, 16 Jun 2020 09:12:04: 8000000 INFO @ Tue, 16 Jun 2020 09:12:10: 14000000 INFO @ Tue, 16 Jun 2020 09:12:11: 12000000 INFO @ Tue, 16 Jun 2020 09:12:14: 9000000 INFO @ Tue, 16 Jun 2020 09:12:20: 15000000 INFO @ Tue, 16 Jun 2020 09:12:20: 13000000 INFO @ Tue, 16 Jun 2020 09:12:23: 10000000 INFO @ Tue, 16 Jun 2020 09:12:30: 14000000 INFO @ Tue, 16 Jun 2020 09:12:30: 16000000 INFO @ Tue, 16 Jun 2020 09:12:33: 11000000 INFO @ Tue, 16 Jun 2020 09:12:39: 15000000 INFO @ Tue, 16 Jun 2020 09:12:40: 17000000 INFO @ Tue, 16 Jun 2020 09:12:42: 12000000 INFO @ Tue, 16 Jun 2020 09:12:49: 16000000 INFO @ Tue, 16 Jun 2020 09:12:50: 18000000 INFO @ Tue, 16 Jun 2020 09:12:51: 13000000 INFO @ Tue, 16 Jun 2020 09:12:58: 17000000 INFO @ Tue, 16 Jun 2020 09:13:00: 19000000 INFO @ Tue, 16 Jun 2020 09:13:01: 14000000 INFO @ Tue, 16 Jun 2020 09:13:07: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:10: 15000000 INFO @ Tue, 16 Jun 2020 09:13:11: 20000000 INFO @ Tue, 16 Jun 2020 09:13:17: 19000000 INFO @ Tue, 16 Jun 2020 09:13:19: 16000000 INFO @ Tue, 16 Jun 2020 09:13:21: 21000000 INFO @ Tue, 16 Jun 2020 09:13:26: 20000000 INFO @ Tue, 16 Jun 2020 09:13:29: 17000000 INFO @ Tue, 16 Jun 2020 09:13:31: 22000000 INFO @ Tue, 16 Jun 2020 09:13:35: 21000000 INFO @ Tue, 16 Jun 2020 09:13:38: 18000000 INFO @ Tue, 16 Jun 2020 09:13:41: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 09:13:41: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 09:13:41: #1 total tags in treatment: 22926685 INFO @ Tue, 16 Jun 2020 09:13:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:41: #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 09:13:41: #1 tags after filtering in treatment: 22926685 INFO @ Tue, 16 Jun 2020 09:13:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:43: #2 number of paired peaks: 176 WARNING @ Tue, 16 Jun 2020 09:13:43: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:13:43: #2 alternative fragment length(s) may be 1,49,70,590,597 bps INFO @ Tue, 16 Jun 2020 09:13:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.05_model.r WARNING @ Tue, 16 Jun 2020 09:13:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:43: #2 You may need to consider one of the other alternative d(s): 1,49,70,590,597 WARNING @ Tue, 16 Jun 2020 09:13:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:13:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:44: 22000000 INFO @ Tue, 16 Jun 2020 09:13:47: 19000000 INFO @ Tue, 16 Jun 2020 09:13:53: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 09:13:53: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 09:13:53: #1 total tags in treatment: 22926685 INFO @ Tue, 16 Jun 2020 09:13:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:53: #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 09:13:53: #1 tags after filtering in treatment: 22926685 INFO @ Tue, 16 Jun 2020 09:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:55: #2 number of paired peaks: 176 WARNING @ Tue, 16 Jun 2020 09:13:55: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:55: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:13:55: #2 alternative fragment length(s) may be 1,49,70,590,597 bps INFO @ Tue, 16 Jun 2020 09:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.10_model.r WARNING @ Tue, 16 Jun 2020 09:13:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:55: #2 You may need to consider one of the other alternative d(s): 1,49,70,590,597 WARNING @ Tue, 16 Jun 2020 09:13:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:13:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:55: 20000000 INFO @ Tue, 16 Jun 2020 09:14:03: 21000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:14:11: 22000000 INFO @ Tue, 16 Jun 2020 09:14:19: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 09:14:19: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 09:14:19: #1 total tags in treatment: 22926685 INFO @ Tue, 16 Jun 2020 09:14:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:19: #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 09:14:19: #1 tags after filtering in treatment: 22926685 INFO @ Tue, 16 Jun 2020 09:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:21: #2 number of paired peaks: 176 WARNING @ Tue, 16 Jun 2020 09:14:21: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:21: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:14:21: #2 alternative fragment length(s) may be 1,49,70,590,597 bps INFO @ Tue, 16 Jun 2020 09:14:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.20_model.r WARNING @ Tue, 16 Jun 2020 09:14:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:14:21: #2 You may need to consider one of the other alternative d(s): 1,49,70,590,597 WARNING @ Tue, 16 Jun 2020 09:14:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:14:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.05_summits.bed INFO @ Tue, 16 Jun 2020 09:14:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.10_summits.bed INFO @ Tue, 16 Jun 2020 09:14:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163952/SRX2163952.20_summits.bed INFO @ Tue, 16 Jun 2020 09:15:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling