Job ID = 6507856 SRX = SRX494939 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:57:57 prefetch.2.10.7: 1) Downloading 'SRR1198471'... 2020-06-26T13:57:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:00:37 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:00:37 prefetch.2.10.7: 1) 'SRR1198471' was downloaded successfully Read 22970231 spots for SRR1198471/SRR1198471.sra Written 22970231 spots for SRR1198471/SRR1198471.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: 00:04:58 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517115 (10.96%) aligned 0 times 16805965 (73.16%) aligned exactly 1 time 3647151 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 2297332 / 20453116 = 0.1123 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 23:12:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.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 23:12:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:12:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:12:14: 1000000 INFO @ Fri, 26 Jun 2020 23:12:18: 2000000 INFO @ Fri, 26 Jun 2020 23:12:23: 3000000 INFO @ Fri, 26 Jun 2020 23:12:28: 4000000 INFO @ Fri, 26 Jun 2020 23:12:33: 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 @ Fri, 26 Jun 2020 23:12:38: 6000000 INFO @ Fri, 26 Jun 2020 23:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.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 23:12:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:12:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:12:43: 7000000 INFO @ Fri, 26 Jun 2020 23:12:44: 1000000 INFO @ Fri, 26 Jun 2020 23:12:49: 8000000 INFO @ Fri, 26 Jun 2020 23:12:49: 2000000 INFO @ Fri, 26 Jun 2020 23:12:54: 9000000 INFO @ Fri, 26 Jun 2020 23:12:55: 3000000 INFO @ Fri, 26 Jun 2020 23:12:59: 10000000 INFO @ Fri, 26 Jun 2020 23:13:01: 4000000 INFO @ Fri, 26 Jun 2020 23:13:05: 11000000 INFO @ Fri, 26 Jun 2020 23:13:06: 5000000 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 23:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.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 23:13:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:13:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:13:10: 12000000 INFO @ Fri, 26 Jun 2020 23:13:12: 6000000 INFO @ Fri, 26 Jun 2020 23:13:15: 1000000 INFO @ Fri, 26 Jun 2020 23:13:16: 13000000 INFO @ Fri, 26 Jun 2020 23:13:17: 7000000 INFO @ Fri, 26 Jun 2020 23:13:21: 2000000 INFO @ Fri, 26 Jun 2020 23:13:21: 14000000 INFO @ Fri, 26 Jun 2020 23:13:22: 8000000 INFO @ Fri, 26 Jun 2020 23:13:26: 15000000 INFO @ Fri, 26 Jun 2020 23:13:27: 3000000 INFO @ Fri, 26 Jun 2020 23:13:28: 9000000 INFO @ Fri, 26 Jun 2020 23:13:32: 16000000 INFO @ Fri, 26 Jun 2020 23:13:33: 4000000 INFO @ Fri, 26 Jun 2020 23:13:34: 10000000 INFO @ Fri, 26 Jun 2020 23:13:38: 17000000 INFO @ Fri, 26 Jun 2020 23:13:40: 5000000 INFO @ Fri, 26 Jun 2020 23:13:40: 11000000 INFO @ Fri, 26 Jun 2020 23:13:43: 18000000 INFO @ Fri, 26 Jun 2020 23:13:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:13:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:13:44: #1 total tags in treatment: 18155784 INFO @ Fri, 26 Jun 2020 23:13:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:13:44: #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 23:13:45: #1 tags after filtering in treatment: 18155784 INFO @ Fri, 26 Jun 2020 23:13:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:13:45: #1 finished! INFO @ Fri, 26 Jun 2020 23:13:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:13:46: 12000000 INFO @ Fri, 26 Jun 2020 23:13:46: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 23:13:46: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 23:13:46: start model_add_line... INFO @ Fri, 26 Jun 2020 23:13:46: start X-correlation... INFO @ Fri, 26 Jun 2020 23:13:46: end of X-cor INFO @ Fri, 26 Jun 2020 23:13:46: #2 finished! INFO @ Fri, 26 Jun 2020 23:13:46: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:13:46: #2 alternative fragment length(s) may be 1,46,538,573 bps INFO @ Fri, 26 Jun 2020 23:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.05_model.r WARNING @ Fri, 26 Jun 2020 23:13:46: #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 23:13:46: #2 You may need to consider one of the other alternative d(s): 1,46,538,573 WARNING @ Fri, 26 Jun 2020 23:13:46: #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 23:13:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:13:47: 6000000 INFO @ Fri, 26 Jun 2020 23:13:52: 13000000 INFO @ Fri, 26 Jun 2020 23:13:53: 7000000 INFO @ Fri, 26 Jun 2020 23:13:57: 14000000 INFO @ Fri, 26 Jun 2020 23:14:00: 8000000 INFO @ Fri, 26 Jun 2020 23:14:03: 15000000 INFO @ Fri, 26 Jun 2020 23:14:07: 9000000 INFO @ Fri, 26 Jun 2020 23:14:09: 16000000 INFO @ Fri, 26 Jun 2020 23:14:13: 10000000 INFO @ Fri, 26 Jun 2020 23:14:14: 17000000 INFO @ Fri, 26 Jun 2020 23:14:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:14:20: 11000000 INFO @ Fri, 26 Jun 2020 23:14:20: 18000000 INFO @ Fri, 26 Jun 2020 23:14:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:14:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:14:21: #1 total tags in treatment: 18155784 INFO @ Fri, 26 Jun 2020 23:14:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:14:21: #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 23:14:22: #1 tags after filtering in treatment: 18155784 INFO @ Fri, 26 Jun 2020 23:14:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:14:22: #1 finished! INFO @ Fri, 26 Jun 2020 23:14:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:14:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:14:23: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 23:14:23: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 23:14:23: start model_add_line... INFO @ Fri, 26 Jun 2020 23:14:23: start X-correlation... INFO @ Fri, 26 Jun 2020 23:14:23: end of X-cor INFO @ Fri, 26 Jun 2020 23:14:23: #2 finished! INFO @ Fri, 26 Jun 2020 23:14:23: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:14:23: #2 alternative fragment length(s) may be 1,46,538,573 bps INFO @ Fri, 26 Jun 2020 23:14:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.10_model.r WARNING @ Fri, 26 Jun 2020 23:14:23: #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 23:14:23: #2 You may need to consider one of the other alternative d(s): 1,46,538,573 WARNING @ Fri, 26 Jun 2020 23:14:23: #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 23:14:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:14:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:14:26: 12000000 INFO @ Fri, 26 Jun 2020 23:14:33: 13000000 INFO @ Fri, 26 Jun 2020 23:14:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:14:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:14:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.05_summits.bed INFO @ Fri, 26 Jun 2020 23:14:35: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:14:39: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:14:45: 15000000 INFO @ Fri, 26 Jun 2020 23:14:52: 16000000 INFO @ Fri, 26 Jun 2020 23:14:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:14:57: 17000000 INFO @ Fri, 26 Jun 2020 23:15:03: 18000000 INFO @ Fri, 26 Jun 2020 23:15:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:15:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:15:05: #1 total tags in treatment: 18155784 INFO @ Fri, 26 Jun 2020 23:15:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:15:05: #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 23:15:05: #1 tags after filtering in treatment: 18155784 INFO @ Fri, 26 Jun 2020 23:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:15:05: #1 finished! INFO @ Fri, 26 Jun 2020 23:15:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:15:06: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 23:15:06: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 23:15:06: start model_add_line... INFO @ Fri, 26 Jun 2020 23:15:06: start X-correlation... INFO @ Fri, 26 Jun 2020 23:15:06: end of X-cor INFO @ Fri, 26 Jun 2020 23:15:06: #2 finished! INFO @ Fri, 26 Jun 2020 23:15:06: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:15:06: #2 alternative fragment length(s) may be 1,46,538,573 bps INFO @ Fri, 26 Jun 2020 23:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.20_model.r WARNING @ Fri, 26 Jun 2020 23:15:06: #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 23:15:06: #2 You may need to consider one of the other alternative d(s): 1,46,538,573 WARNING @ Fri, 26 Jun 2020 23:15:06: #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 23:15:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:15:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:15:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:15:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.10_summits.bed INFO @ Fri, 26 Jun 2020 23:15:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:15:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:15:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:15:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:15:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494939/SRX494939.20_summits.bed INFO @ Fri, 26 Jun 2020 23:15:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling