Job ID = 6368953 SRX = SRX7627554 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:40:17 prefetch.2.10.7: 1) Downloading 'SRR10961902'... 2020-06-16T00:40:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:36 prefetch.2.10.7: 1) 'SRR10961902' was downloaded successfully Read 25839740 spots for SRR10961902/SRR10961902.sra Written 25839740 spots for SRR10961902/SRR10961902.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: 00:06:24 25839740 reads; of these: 25839740 (100.00%) were unpaired; of these: 1337199 (5.17%) aligned 0 times 18061535 (69.90%) aligned exactly 1 time 6441006 (24.93%) aligned >1 times 94.83% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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] 4109032 / 24502541 = 0.1677 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 09:59:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.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 09:59:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:54: 1000000 INFO @ Tue, 16 Jun 2020 09:59:59: 2000000 INFO @ Tue, 16 Jun 2020 10:00:04: 3000000 INFO @ Tue, 16 Jun 2020 10:00:09: 4000000 INFO @ Tue, 16 Jun 2020 10:00:14: 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 10:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.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 10:00:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:00:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:00:19: 6000000 INFO @ Tue, 16 Jun 2020 10:00:24: 7000000 INFO @ Tue, 16 Jun 2020 10:00:24: 1000000 INFO @ Tue, 16 Jun 2020 10:00:29: 8000000 INFO @ Tue, 16 Jun 2020 10:00:30: 2000000 INFO @ Tue, 16 Jun 2020 10:00:35: 9000000 INFO @ Tue, 16 Jun 2020 10:00:36: 3000000 INFO @ Tue, 16 Jun 2020 10:00:40: 10000000 INFO @ Tue, 16 Jun 2020 10:00:42: 4000000 INFO @ Tue, 16 Jun 2020 10:00:45: 11000000 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 10:00:48: 5000000 INFO @ Tue, 16 Jun 2020 10:00:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.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 10:00:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:00:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:00:50: 12000000 INFO @ Tue, 16 Jun 2020 10:00:54: 6000000 INFO @ Tue, 16 Jun 2020 10:00:54: 1000000 INFO @ Tue, 16 Jun 2020 10:00:55: 13000000 INFO @ Tue, 16 Jun 2020 10:00:59: 7000000 INFO @ Tue, 16 Jun 2020 10:00:59: 2000000 INFO @ Tue, 16 Jun 2020 10:01:01: 14000000 INFO @ Tue, 16 Jun 2020 10:01:04: 8000000 INFO @ Tue, 16 Jun 2020 10:01:05: 3000000 INFO @ Tue, 16 Jun 2020 10:01:06: 15000000 INFO @ Tue, 16 Jun 2020 10:01:10: 4000000 INFO @ Tue, 16 Jun 2020 10:01:10: 9000000 INFO @ Tue, 16 Jun 2020 10:01:11: 16000000 INFO @ Tue, 16 Jun 2020 10:01:15: 5000000 INFO @ Tue, 16 Jun 2020 10:01:16: 10000000 INFO @ Tue, 16 Jun 2020 10:01:16: 17000000 INFO @ Tue, 16 Jun 2020 10:01:20: 6000000 INFO @ Tue, 16 Jun 2020 10:01:22: 18000000 INFO @ Tue, 16 Jun 2020 10:01:22: 11000000 INFO @ Tue, 16 Jun 2020 10:01:26: 7000000 INFO @ Tue, 16 Jun 2020 10:01:27: 19000000 INFO @ Tue, 16 Jun 2020 10:01:28: 12000000 INFO @ Tue, 16 Jun 2020 10:01:31: 8000000 INFO @ Tue, 16 Jun 2020 10:01:32: 20000000 INFO @ Tue, 16 Jun 2020 10:01:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:01:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:01:34: #1 total tags in treatment: 20393509 INFO @ Tue, 16 Jun 2020 10:01:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:34: #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 10:01:34: 13000000 INFO @ Tue, 16 Jun 2020 10:01:34: #1 tags after filtering in treatment: 20393509 INFO @ Tue, 16 Jun 2020 10:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:34: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:36: #2 number of paired peaks: 380 WARNING @ Tue, 16 Jun 2020 10:01:36: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:36: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:36: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:36: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:36: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:36: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:01:36: #2 alternative fragment length(s) may be 1,22 bps INFO @ Tue, 16 Jun 2020 10:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.05_model.r WARNING @ Tue, 16 Jun 2020 10:01:36: #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 10:01:36: #2 You may need to consider one of the other alternative d(s): 1,22 WARNING @ Tue, 16 Jun 2020 10:01:36: #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 10:01:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:36: 9000000 INFO @ Tue, 16 Jun 2020 10:01:40: 14000000 INFO @ Tue, 16 Jun 2020 10:01:41: 10000000 INFO @ Tue, 16 Jun 2020 10:01:46: 15000000 INFO @ Tue, 16 Jun 2020 10:01:47: 11000000 INFO @ Tue, 16 Jun 2020 10:01:52: 16000000 INFO @ Tue, 16 Jun 2020 10:01:52: 12000000 INFO @ Tue, 16 Jun 2020 10:01:57: 13000000 INFO @ Tue, 16 Jun 2020 10:01:58: 17000000 INFO @ Tue, 16 Jun 2020 10:02:03: 14000000 INFO @ Tue, 16 Jun 2020 10:02:04: 18000000 INFO @ Tue, 16 Jun 2020 10:02:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:02:08: 15000000 INFO @ Tue, 16 Jun 2020 10:02:10: 19000000 INFO @ Tue, 16 Jun 2020 10:02:13: 16000000 INFO @ Tue, 16 Jun 2020 10:02:16: 20000000 INFO @ Tue, 16 Jun 2020 10:02:18: 17000000 INFO @ Tue, 16 Jun 2020 10:02:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:02:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:02:19: #1 total tags in treatment: 20393509 INFO @ Tue, 16 Jun 2020 10:02:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:19: #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 10:02:19: #1 tags after filtering in treatment: 20393509 INFO @ Tue, 16 Jun 2020 10:02:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:02:19: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:20: #2 number of paired peaks: 380 WARNING @ Tue, 16 Jun 2020 10:02:20: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Tue, 16 Jun 2020 10:02:20: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:21: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:21: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:21: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:21: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:02:21: #2 alternative fragment length(s) may be 1,22 bps INFO @ Tue, 16 Jun 2020 10:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.10_model.r WARNING @ Tue, 16 Jun 2020 10:02:21: #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 10:02:21: #2 You may need to consider one of the other alternative d(s): 1,22 WARNING @ Tue, 16 Jun 2020 10:02:21: #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 10:02:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:23: 18000000 INFO @ Tue, 16 Jun 2020 10:02:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.05_summits.bed INFO @ Tue, 16 Jun 2020 10:02:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:29: 19000000 INFO @ Tue, 16 Jun 2020 10:02:34: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:02:36: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:02:36: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:02:36: #1 total tags in treatment: 20393509 INFO @ Tue, 16 Jun 2020 10:02:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:36: #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 10:02:36: #1 tags after filtering in treatment: 20393509 INFO @ Tue, 16 Jun 2020 10:02:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:02:36: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:37: #2 number of paired peaks: 380 WARNING @ Tue, 16 Jun 2020 10:02:37: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Tue, 16 Jun 2020 10:02:37: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:38: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:38: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:38: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:38: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:02:38: #2 alternative fragment length(s) may be 1,22 bps INFO @ Tue, 16 Jun 2020 10:02:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.20_model.r WARNING @ Tue, 16 Jun 2020 10:02:38: #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 10:02:38: #2 You may need to consider one of the other alternative d(s): 1,22 WARNING @ Tue, 16 Jun 2020 10:02:38: #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 10:02:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.10_summits.bed INFO @ Tue, 16 Jun 2020 10:03:10: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627554/SRX7627554.20_summits.bed INFO @ Tue, 16 Jun 2020 10:03:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling