Job ID = 6367018 SRX = SRX2710279 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:08:08 prefetch.2.10.7: 1) Downloading 'SRR5418733'... 2020-06-15T23:08:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:46 prefetch.2.10.7: 1) 'SRR5418733' was downloaded successfully Read 53428231 spots for SRR5418733/SRR5418733.sra Written 53428231 spots for SRR5418733/SRR5418733.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: 00:24:06 53428231 reads; of these: 53428231 (100.00%) were unpaired; of these: 5533535 (10.36%) aligned 0 times 28965313 (54.21%) aligned exactly 1 time 18929383 (35.43%) aligned >1 times 89.64% overall alignment rate Time searching: 00:24:06 Overall time: 00:24:06 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 20 files... [bam_rmdupse_core] 24834610 / 47894696 = 0.5185 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 08:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.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 08:55:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:31: 1000000 INFO @ Tue, 16 Jun 2020 08:55:41: 2000000 INFO @ Tue, 16 Jun 2020 08:55:50: 3000000 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 08:55:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.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 08:55:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:00: 4000000 INFO @ Tue, 16 Jun 2020 08:56:03: 1000000 INFO @ Tue, 16 Jun 2020 08:56:11: 5000000 INFO @ Tue, 16 Jun 2020 08:56:13: 2000000 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 08:56:21: 6000000 INFO @ Tue, 16 Jun 2020 08:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.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 08:56:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:23: 3000000 INFO @ Tue, 16 Jun 2020 08:56:32: 7000000 INFO @ Tue, 16 Jun 2020 08:56:33: 1000000 INFO @ Tue, 16 Jun 2020 08:56:34: 4000000 INFO @ Tue, 16 Jun 2020 08:56:43: 8000000 INFO @ Tue, 16 Jun 2020 08:56:44: 2000000 INFO @ Tue, 16 Jun 2020 08:56:45: 5000000 INFO @ Tue, 16 Jun 2020 08:56:54: 9000000 INFO @ Tue, 16 Jun 2020 08:56:55: 3000000 INFO @ Tue, 16 Jun 2020 08:56:56: 6000000 INFO @ Tue, 16 Jun 2020 08:57:05: 10000000 INFO @ Tue, 16 Jun 2020 08:57:06: 4000000 INFO @ Tue, 16 Jun 2020 08:57:07: 7000000 INFO @ Tue, 16 Jun 2020 08:57:16: 11000000 INFO @ Tue, 16 Jun 2020 08:57:17: 5000000 INFO @ Tue, 16 Jun 2020 08:57:18: 8000000 INFO @ Tue, 16 Jun 2020 08:57:26: 12000000 INFO @ Tue, 16 Jun 2020 08:57:28: 6000000 INFO @ Tue, 16 Jun 2020 08:57:29: 9000000 INFO @ Tue, 16 Jun 2020 08:57:37: 13000000 INFO @ Tue, 16 Jun 2020 08:57:39: 7000000 INFO @ Tue, 16 Jun 2020 08:57:39: 10000000 INFO @ Tue, 16 Jun 2020 08:57:48: 14000000 INFO @ Tue, 16 Jun 2020 08:57:50: 8000000 INFO @ Tue, 16 Jun 2020 08:57:50: 11000000 INFO @ Tue, 16 Jun 2020 08:57:58: 15000000 INFO @ Tue, 16 Jun 2020 08:58:00: 12000000 INFO @ Tue, 16 Jun 2020 08:58:00: 9000000 INFO @ Tue, 16 Jun 2020 08:58:09: 16000000 INFO @ Tue, 16 Jun 2020 08:58:11: 13000000 INFO @ Tue, 16 Jun 2020 08:58:11: 10000000 INFO @ Tue, 16 Jun 2020 08:58:19: 17000000 INFO @ Tue, 16 Jun 2020 08:58:21: 14000000 INFO @ Tue, 16 Jun 2020 08:58:21: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:58:30: 18000000 INFO @ Tue, 16 Jun 2020 08:58:31: 15000000 INFO @ Tue, 16 Jun 2020 08:58:32: 12000000 INFO @ Tue, 16 Jun 2020 08:58:40: 19000000 INFO @ Tue, 16 Jun 2020 08:58:42: 16000000 INFO @ Tue, 16 Jun 2020 08:58:43: 13000000 INFO @ Tue, 16 Jun 2020 08:58:51: 20000000 INFO @ Tue, 16 Jun 2020 08:58:52: 17000000 INFO @ Tue, 16 Jun 2020 08:58:53: 14000000 INFO @ Tue, 16 Jun 2020 08:59:01: 21000000 INFO @ Tue, 16 Jun 2020 08:59:02: 18000000 INFO @ Tue, 16 Jun 2020 08:59:04: 15000000 INFO @ Tue, 16 Jun 2020 08:59:11: 22000000 INFO @ Tue, 16 Jun 2020 08:59:12: 19000000 INFO @ Tue, 16 Jun 2020 08:59:14: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:59:22: 23000000 INFO @ Tue, 16 Jun 2020 08:59:22: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:59:22: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:59:22: #1 total tags in treatment: 23060086 INFO @ Tue, 16 Jun 2020 08:59:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:22: #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 08:59:23: 20000000 INFO @ Tue, 16 Jun 2020 08:59:23: #1 tags after filtering in treatment: 23060086 INFO @ Tue, 16 Jun 2020 08:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:24: 17000000 INFO @ Tue, 16 Jun 2020 08:59:25: #2 number of paired peaks: 502 WARNING @ Tue, 16 Jun 2020 08:59:25: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:25: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:59:25: #2 alternative fragment length(s) may be 2,53 bps INFO @ Tue, 16 Jun 2020 08:59:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.05_model.r WARNING @ Tue, 16 Jun 2020 08:59:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:59:25: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Tue, 16 Jun 2020 08:59:25: #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 08:59:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:33: 21000000 INFO @ Tue, 16 Jun 2020 08:59:35: 18000000 INFO @ Tue, 16 Jun 2020 08:59:43: 22000000 INFO @ Tue, 16 Jun 2020 08:59:45: 19000000 INFO @ Tue, 16 Jun 2020 08:59:52: 23000000 INFO @ Tue, 16 Jun 2020 08:59:53: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:59:53: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:59:53: #1 total tags in treatment: 23060086 INFO @ Tue, 16 Jun 2020 08:59:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:53: #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 08:59:54: #1 tags after filtering in treatment: 23060086 INFO @ Tue, 16 Jun 2020 08:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:55: #2 number of paired peaks: 502 WARNING @ Tue, 16 Jun 2020 08:59:55: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:55: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:59:55: #2 alternative fragment length(s) may be 2,53 bps INFO @ Tue, 16 Jun 2020 08:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.10_model.r WARNING @ Tue, 16 Jun 2020 08:59:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:59:55: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Tue, 16 Jun 2020 08:59:55: #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 08:59:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:56: 20000000 INFO @ Tue, 16 Jun 2020 09:00:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:05: 21000000 INFO @ Tue, 16 Jun 2020 09:00:14: 22000000 INFO @ Tue, 16 Jun 2020 09:00:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.05_summits.bed INFO @ Tue, 16 Jun 2020 09:00:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:23: 23000000 INFO @ Tue, 16 Jun 2020 09:00:24: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:00:24: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:00:24: #1 total tags in treatment: 23060086 INFO @ Tue, 16 Jun 2020 09:00:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:24: #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 09:00:24: #1 tags after filtering in treatment: 23060086 INFO @ Tue, 16 Jun 2020 09:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:26: #2 number of paired peaks: 502 WARNING @ Tue, 16 Jun 2020 09:00:26: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:26: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:00:26: #2 alternative fragment length(s) may be 2,53 bps INFO @ Tue, 16 Jun 2020 09:00:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.20_model.r WARNING @ Tue, 16 Jun 2020 09:00:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:26: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Tue, 16 Jun 2020 09:00:26: #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 09:00:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.10_summits.bed INFO @ Tue, 16 Jun 2020 09:00:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710279/SRX2710279.20_summits.bed INFO @ Tue, 16 Jun 2020 09:01:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling