Job ID = 6366515 SRX = SRX1674095 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:50:56 prefetch.2.10.7: 1) Downloading 'SRR3320141'... 2020-06-15T22:50:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:00 prefetch.2.10.7: 1) 'SRR3320141' was downloaded successfully Read 85546882 spots for SRR3320141/SRR3320141.sra Written 85546882 spots for SRR3320141/SRR3320141.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: 00:17:40 85546882 reads; of these: 85546882 (100.00%) were unpaired; of these: 12026434 (14.06%) aligned 0 times 60962522 (71.26%) aligned exactly 1 time 12557926 (14.68%) aligned >1 times 85.94% overall alignment rate Time searching: 00:17:40 Overall time: 00:17:40 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 32 files... [bam_rmdupse_core] 52631008 / 73520448 = 0.7159 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 08:32:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.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 08:32:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:39: 1000000 INFO @ Tue, 16 Jun 2020 08:32:44: 2000000 INFO @ Tue, 16 Jun 2020 08:32:49: 3000000 INFO @ Tue, 16 Jun 2020 08:32:54: 4000000 INFO @ Tue, 16 Jun 2020 08:32:58: 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 08:33:03: 6000000 INFO @ Tue, 16 Jun 2020 08:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.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 08:33:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:09: 7000000 INFO @ Tue, 16 Jun 2020 08:33:09: 1000000 INFO @ Tue, 16 Jun 2020 08:33:14: 8000000 INFO @ Tue, 16 Jun 2020 08:33:14: 2000000 INFO @ Tue, 16 Jun 2020 08:33:20: 3000000 INFO @ Tue, 16 Jun 2020 08:33:20: 9000000 INFO @ Tue, 16 Jun 2020 08:33:25: 4000000 INFO @ Tue, 16 Jun 2020 08:33:25: 10000000 INFO @ Tue, 16 Jun 2020 08:33:30: 5000000 INFO @ Tue, 16 Jun 2020 08:33:30: 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 08:33:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.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 08:33:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:36: 6000000 INFO @ Tue, 16 Jun 2020 08:33:36: 12000000 INFO @ Tue, 16 Jun 2020 08:33:39: 1000000 INFO @ Tue, 16 Jun 2020 08:33:41: 7000000 INFO @ Tue, 16 Jun 2020 08:33:41: 13000000 INFO @ Tue, 16 Jun 2020 08:33:44: 2000000 INFO @ Tue, 16 Jun 2020 08:33:46: 8000000 INFO @ Tue, 16 Jun 2020 08:33:46: 14000000 INFO @ Tue, 16 Jun 2020 08:33:50: 3000000 INFO @ Tue, 16 Jun 2020 08:33:52: 9000000 INFO @ Tue, 16 Jun 2020 08:33:52: 15000000 INFO @ Tue, 16 Jun 2020 08:33:55: 4000000 INFO @ Tue, 16 Jun 2020 08:33:57: 16000000 INFO @ Tue, 16 Jun 2020 08:33:57: 10000000 INFO @ Tue, 16 Jun 2020 08:34:00: 5000000 INFO @ Tue, 16 Jun 2020 08:34:02: 17000000 INFO @ Tue, 16 Jun 2020 08:34:02: 11000000 INFO @ Tue, 16 Jun 2020 08:34:06: 6000000 INFO @ Tue, 16 Jun 2020 08:34:07: 18000000 INFO @ Tue, 16 Jun 2020 08:34:08: 12000000 INFO @ Tue, 16 Jun 2020 08:34:11: 7000000 INFO @ Tue, 16 Jun 2020 08:34:13: 19000000 INFO @ Tue, 16 Jun 2020 08:34:13: 13000000 INFO @ Tue, 16 Jun 2020 08:34:16: 8000000 INFO @ Tue, 16 Jun 2020 08:34:18: 20000000 INFO @ Tue, 16 Jun 2020 08:34:18: 14000000 INFO @ Tue, 16 Jun 2020 08:34:22: 9000000 INFO @ Tue, 16 Jun 2020 08:34:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:34:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:34:23: #1 total tags in treatment: 20889440 INFO @ Tue, 16 Jun 2020 08:34:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:23: #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 08:34:23: #1 tags after filtering in treatment: 20889440 INFO @ Tue, 16 Jun 2020 08:34:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:24: 15000000 INFO @ Tue, 16 Jun 2020 08:34:24: #2 number of paired peaks: 370 WARNING @ Tue, 16 Jun 2020 08:34:24: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:25: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:34:25: #2 alternative fragment length(s) may be 1,595 bps INFO @ Tue, 16 Jun 2020 08:34:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.05_model.r WARNING @ Tue, 16 Jun 2020 08:34:25: #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 08:34:25: #2 You may need to consider one of the other alternative d(s): 1,595 WARNING @ Tue, 16 Jun 2020 08:34:25: #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 08:34:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:27: 10000000 INFO @ Tue, 16 Jun 2020 08:34:29: 16000000 INFO @ Tue, 16 Jun 2020 08:34:32: 11000000 INFO @ Tue, 16 Jun 2020 08:34:34: 17000000 INFO @ Tue, 16 Jun 2020 08:34:38: 12000000 INFO @ Tue, 16 Jun 2020 08:34:39: 18000000 INFO @ Tue, 16 Jun 2020 08:34:43: 13000000 INFO @ Tue, 16 Jun 2020 08:34:45: 19000000 INFO @ Tue, 16 Jun 2020 08:34:48: 14000000 INFO @ Tue, 16 Jun 2020 08:34:50: 20000000 INFO @ Tue, 16 Jun 2020 08:34:54: 15000000 INFO @ Tue, 16 Jun 2020 08:34:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:34:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:34:55: #1 total tags in treatment: 20889440 INFO @ Tue, 16 Jun 2020 08:34:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:55: #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 08:34:55: #1 tags after filtering in treatment: 20889440 INFO @ Tue, 16 Jun 2020 08:34:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:56: #2 number of paired peaks: 370 WARNING @ Tue, 16 Jun 2020 08:34:56: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:57: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:34:57: #2 alternative fragment length(s) may be 1,595 bps INFO @ Tue, 16 Jun 2020 08:34:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.10_model.r WARNING @ Tue, 16 Jun 2020 08:34:57: #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 08:34:57: #2 You may need to consider one of the other alternative d(s): 1,595 WARNING @ Tue, 16 Jun 2020 08:34:57: #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 08:34:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:59: 16000000 INFO @ Tue, 16 Jun 2020 08:35:04: 17000000 INFO @ Tue, 16 Jun 2020 08:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.05_summits.bed INFO @ Tue, 16 Jun 2020 08:35:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:09: 18000000 INFO @ Tue, 16 Jun 2020 08:35:14: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:20: 20000000 INFO @ Tue, 16 Jun 2020 08:35:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:35:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:35:24: #1 total tags in treatment: 20889440 INFO @ Tue, 16 Jun 2020 08:35:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:24: #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 08:35:25: #1 tags after filtering in treatment: 20889440 INFO @ Tue, 16 Jun 2020 08:35:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:26: #2 number of paired peaks: 370 WARNING @ Tue, 16 Jun 2020 08:35:26: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:26: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:35:26: #2 alternative fragment length(s) may be 1,595 bps INFO @ Tue, 16 Jun 2020 08:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.20_model.r WARNING @ Tue, 16 Jun 2020 08:35:26: #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 08:35:26: #2 You may need to consider one of the other alternative d(s): 1,595 WARNING @ Tue, 16 Jun 2020 08:35:26: #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 08:35:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674095/SRX1674095.20_summits.bed INFO @ Tue, 16 Jun 2020 08:36:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling