Job ID = 6507827 SRX = SRX494831 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:10:41 prefetch.2.10.7: 1) Downloading 'SRR1198363'... 2020-06-26T14:10:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:13:00 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:13:00 prefetch.2.10.7: 1) 'SRR1198363' was downloaded successfully Read 27717782 spots for SRR1198363/SRR1198363.sra Written 27717782 spots for SRR1198363/SRR1198363.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: 00:04:16 27717782 reads; of these: 27717782 (100.00%) were unpaired; of these: 5102490 (18.41%) aligned 0 times 18379191 (66.31%) aligned exactly 1 time 4236101 (15.28%) aligned >1 times 81.59% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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 8 files... [bam_rmdupse_core] 3124057 / 22615292 = 0.1381 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 @ Fri, 26 Jun 2020 23:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.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 @ Fri, 26 Jun 2020 23:23:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:23:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:23:32: 1000000 INFO @ Fri, 26 Jun 2020 23:23:38: 2000000 INFO @ Fri, 26 Jun 2020 23:23:43: 3000000 INFO @ Fri, 26 Jun 2020 23:23:49: 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 @ Fri, 26 Jun 2020 23:23:55: 5000000 INFO @ Fri, 26 Jun 2020 23:23:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.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 @ Fri, 26 Jun 2020 23:23:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:23:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:24:01: 6000000 INFO @ Fri, 26 Jun 2020 23:24:03: 1000000 INFO @ Fri, 26 Jun 2020 23:24:07: 7000000 INFO @ Fri, 26 Jun 2020 23:24:09: 2000000 INFO @ Fri, 26 Jun 2020 23:24:13: 8000000 INFO @ Fri, 26 Jun 2020 23:24:15: 3000000 INFO @ Fri, 26 Jun 2020 23:24:19: 9000000 INFO @ Fri, 26 Jun 2020 23:24:21: 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 @ Fri, 26 Jun 2020 23:24:25: 10000000 INFO @ Fri, 26 Jun 2020 23:24:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.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 @ Fri, 26 Jun 2020 23:24:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:24:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:24:28: 5000000 INFO @ Fri, 26 Jun 2020 23:24:31: 11000000 INFO @ Fri, 26 Jun 2020 23:24:33: 1000000 INFO @ Fri, 26 Jun 2020 23:24:34: 6000000 INFO @ Fri, 26 Jun 2020 23:24:37: 12000000 INFO @ Fri, 26 Jun 2020 23:24:39: 2000000 INFO @ Fri, 26 Jun 2020 23:24:40: 7000000 INFO @ Fri, 26 Jun 2020 23:24:44: 13000000 INFO @ Fri, 26 Jun 2020 23:24:45: 3000000 INFO @ Fri, 26 Jun 2020 23:24:46: 8000000 INFO @ Fri, 26 Jun 2020 23:24:50: 14000000 INFO @ Fri, 26 Jun 2020 23:24:52: 4000000 INFO @ Fri, 26 Jun 2020 23:24:53: 9000000 INFO @ Fri, 26 Jun 2020 23:24:56: 15000000 INFO @ Fri, 26 Jun 2020 23:24:59: 5000000 INFO @ Fri, 26 Jun 2020 23:25:00: 10000000 INFO @ Fri, 26 Jun 2020 23:25:03: 16000000 INFO @ Fri, 26 Jun 2020 23:25:06: 6000000 INFO @ Fri, 26 Jun 2020 23:25:06: 11000000 INFO @ Fri, 26 Jun 2020 23:25:09: 17000000 INFO @ Fri, 26 Jun 2020 23:25:12: 7000000 INFO @ Fri, 26 Jun 2020 23:25:13: 12000000 INFO @ Fri, 26 Jun 2020 23:25:16: 18000000 INFO @ Fri, 26 Jun 2020 23:25:20: 8000000 INFO @ Fri, 26 Jun 2020 23:25:20: 13000000 INFO @ Fri, 26 Jun 2020 23:25:22: 19000000 INFO @ Fri, 26 Jun 2020 23:25:25: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:25:25: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:25:25: #1 total tags in treatment: 19491235 INFO @ Fri, 26 Jun 2020 23:25:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:25:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:25:25: #1 tags after filtering in treatment: 19491235 INFO @ Fri, 26 Jun 2020 23:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:25:25: #1 finished! INFO @ Fri, 26 Jun 2020 23:25:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:25:26: 9000000 INFO @ Fri, 26 Jun 2020 23:25:26: 14000000 INFO @ Fri, 26 Jun 2020 23:25:27: #2 number of paired peaks: 229 WARNING @ Fri, 26 Jun 2020 23:25:27: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 26 Jun 2020 23:25:27: start model_add_line... INFO @ Fri, 26 Jun 2020 23:25:27: start X-correlation... INFO @ Fri, 26 Jun 2020 23:25:27: end of X-cor INFO @ Fri, 26 Jun 2020 23:25:27: #2 finished! INFO @ Fri, 26 Jun 2020 23:25:27: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:25:27: #2 alternative fragment length(s) may be 1,33,410,554,572 bps INFO @ Fri, 26 Jun 2020 23:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.05_model.r WARNING @ Fri, 26 Jun 2020 23:25:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:25:27: #2 You may need to consider one of the other alternative d(s): 1,33,410,554,572 WARNING @ Fri, 26 Jun 2020 23:25:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:25:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:25:33: 15000000 INFO @ Fri, 26 Jun 2020 23:25:33: 10000000 INFO @ Fri, 26 Jun 2020 23:25:39: 16000000 INFO @ Fri, 26 Jun 2020 23:25:39: 11000000 INFO @ Fri, 26 Jun 2020 23:25:46: 17000000 INFO @ Fri, 26 Jun 2020 23:25:46: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:25:52: 18000000 INFO @ Fri, 26 Jun 2020 23:25:52: 13000000 INFO @ Fri, 26 Jun 2020 23:25:58: 19000000 INFO @ Fri, 26 Jun 2020 23:25:58: 14000000 INFO @ Fri, 26 Jun 2020 23:26:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:26:01: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:26:01: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:26:01: #1 total tags in treatment: 19491235 INFO @ Fri, 26 Jun 2020 23:26:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:26:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:26:02: #1 tags after filtering in treatment: 19491235 INFO @ Fri, 26 Jun 2020 23:26:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:26:02: #1 finished! INFO @ Fri, 26 Jun 2020 23:26:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:26:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:26:03: #2 number of paired peaks: 229 WARNING @ Fri, 26 Jun 2020 23:26:03: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 26 Jun 2020 23:26:03: start model_add_line... INFO @ Fri, 26 Jun 2020 23:26:03: start X-correlation... INFO @ Fri, 26 Jun 2020 23:26:03: end of X-cor INFO @ Fri, 26 Jun 2020 23:26:03: #2 finished! INFO @ Fri, 26 Jun 2020 23:26:03: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:26:03: #2 alternative fragment length(s) may be 1,33,410,554,572 bps INFO @ Fri, 26 Jun 2020 23:26:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.10_model.r WARNING @ Fri, 26 Jun 2020 23:26:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:26:03: #2 You may need to consider one of the other alternative d(s): 1,33,410,554,572 WARNING @ Fri, 26 Jun 2020 23:26:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:26:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:26:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:26:05: 15000000 INFO @ Fri, 26 Jun 2020 23:26:11: 16000000 INFO @ Fri, 26 Jun 2020 23:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.05_summits.bed INFO @ Fri, 26 Jun 2020 23:26:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:26:16: 17000000 INFO @ Fri, 26 Jun 2020 23:26:22: 18000000 INFO @ Fri, 26 Jun 2020 23:26:28: 19000000 INFO @ Fri, 26 Jun 2020 23:26:30: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:26:30: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:26:30: #1 total tags in treatment: 19491235 INFO @ Fri, 26 Jun 2020 23:26:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:26:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:26:31: #1 tags after filtering in treatment: 19491235 INFO @ Fri, 26 Jun 2020 23:26:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:26:31: #1 finished! INFO @ Fri, 26 Jun 2020 23:26:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:26:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:26:32: #2 number of paired peaks: 229 WARNING @ Fri, 26 Jun 2020 23:26:32: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 26 Jun 2020 23:26:32: start model_add_line... INFO @ Fri, 26 Jun 2020 23:26:32: start X-correlation... INFO @ Fri, 26 Jun 2020 23:26:32: end of X-cor INFO @ Fri, 26 Jun 2020 23:26:32: #2 finished! INFO @ Fri, 26 Jun 2020 23:26:32: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:26:32: #2 alternative fragment length(s) may be 1,33,410,554,572 bps INFO @ Fri, 26 Jun 2020 23:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.20_model.r WARNING @ Fri, 26 Jun 2020 23:26:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:26:32: #2 You may need to consider one of the other alternative d(s): 1,33,410,554,572 WARNING @ Fri, 26 Jun 2020 23:26:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:26:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:26:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:26:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.10_summits.bed INFO @ Fri, 26 Jun 2020 23:26:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:27:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:27:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494831/SRX494831.20_summits.bed INFO @ Fri, 26 Jun 2020 23:27:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling