Job ID = 12265093 SRX = SRX2969571 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:01 Multiseed full-index search: 00:07:53 34363329 reads; of these: 34363329 (100.00%) were unpaired; of these: 2202888 (6.41%) aligned 0 times 27329799 (79.53%) aligned exactly 1 time 4830642 (14.06%) aligned >1 times 93.59% overall alignment rate Time searching: 00:07:54 Overall time: 00:07:54 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 16 files... [bam_rmdupse_core] 19158033 / 32160441 = 0.5957 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:21:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.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 @ Sat, 03 Apr 2021 06:21:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:21:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:21:37: 1000000 INFO @ Sat, 03 Apr 2021 06:21:43: 2000000 INFO @ Sat, 03 Apr 2021 06:21:50: 3000000 INFO @ Sat, 03 Apr 2021 06:21:56: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:22:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.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 @ Sat, 03 Apr 2021 06:22:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:22:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:22:03: 5000000 INFO @ Sat, 03 Apr 2021 06:22:07: 1000000 INFO @ Sat, 03 Apr 2021 06:22:10: 6000000 INFO @ Sat, 03 Apr 2021 06:22:13: 2000000 INFO @ Sat, 03 Apr 2021 06:22:16: 7000000 INFO @ Sat, 03 Apr 2021 06:22:19: 3000000 INFO @ Sat, 03 Apr 2021 06:22:23: 8000000 INFO @ Sat, 03 Apr 2021 06:22:26: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:22:30: 9000000 INFO @ Sat, 03 Apr 2021 06:22:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.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 @ Sat, 03 Apr 2021 06:22:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:22:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:22:32: 5000000 INFO @ Sat, 03 Apr 2021 06:22:37: 10000000 INFO @ Sat, 03 Apr 2021 06:22:37: 1000000 INFO @ Sat, 03 Apr 2021 06:22:39: 6000000 INFO @ Sat, 03 Apr 2021 06:22:44: 11000000 INFO @ Sat, 03 Apr 2021 06:22:44: 2000000 INFO @ Sat, 03 Apr 2021 06:22:45: 7000000 INFO @ Sat, 03 Apr 2021 06:22:51: 12000000 INFO @ Sat, 03 Apr 2021 06:22:51: 3000000 INFO @ Sat, 03 Apr 2021 06:22:52: 8000000 INFO @ Sat, 03 Apr 2021 06:22:57: 13000000 INFO @ Sat, 03 Apr 2021 06:22:57: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:22:57: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:22:57: #1 total tags in treatment: 13002408 INFO @ Sat, 03 Apr 2021 06:22:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:22:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:22:58: #1 tags after filtering in treatment: 13002408 INFO @ Sat, 03 Apr 2021 06:22:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:22:58: #1 finished! INFO @ Sat, 03 Apr 2021 06:22:58: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:22:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:22:58: 9000000 INFO @ Sat, 03 Apr 2021 06:22:58: 4000000 INFO @ Sat, 03 Apr 2021 06:22:58: #2 number of paired peaks: 196 WARNING @ Sat, 03 Apr 2021 06:22:58: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 03 Apr 2021 06:22:58: start model_add_line... INFO @ Sat, 03 Apr 2021 06:22:59: start X-correlation... INFO @ Sat, 03 Apr 2021 06:22:59: end of X-cor INFO @ Sat, 03 Apr 2021 06:22:59: #2 finished! INFO @ Sat, 03 Apr 2021 06:22:59: #2 predicted fragment length is 2 bps INFO @ Sat, 03 Apr 2021 06:22:59: #2 alternative fragment length(s) may be 2,12,52 bps INFO @ Sat, 03 Apr 2021 06:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.05_model.r WARNING @ Sat, 03 Apr 2021 06:22:59: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:22:59: #2 You may need to consider one of the other alternative d(s): 2,12,52 WARNING @ Sat, 03 Apr 2021 06:22:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:22:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:23:04: 10000000 INFO @ Sat, 03 Apr 2021 06:23:05: 5000000 INFO @ Sat, 03 Apr 2021 06:23:10: 11000000 INFO @ Sat, 03 Apr 2021 06:23:12: 6000000 INFO @ Sat, 03 Apr 2021 06:23:16: 12000000 INFO @ Sat, 03 Apr 2021 06:23:19: 7000000 INFO @ Sat, 03 Apr 2021 06:23:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:23:22: 13000000 INFO @ Sat, 03 Apr 2021 06:23:22: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:23:22: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:23:22: #1 total tags in treatment: 13002408 INFO @ Sat, 03 Apr 2021 06:23:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:23:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:23:23: #1 tags after filtering in treatment: 13002408 INFO @ Sat, 03 Apr 2021 06:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:23:23: #1 finished! INFO @ Sat, 03 Apr 2021 06:23:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:23:23: #2 number of paired peaks: 196 WARNING @ Sat, 03 Apr 2021 06:23:23: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 03 Apr 2021 06:23:23: start model_add_line... INFO @ Sat, 03 Apr 2021 06:23:24: start X-correlation... INFO @ Sat, 03 Apr 2021 06:23:24: end of X-cor INFO @ Sat, 03 Apr 2021 06:23:24: #2 finished! INFO @ Sat, 03 Apr 2021 06:23:24: #2 predicted fragment length is 2 bps INFO @ Sat, 03 Apr 2021 06:23:24: #2 alternative fragment length(s) may be 2,12,52 bps INFO @ Sat, 03 Apr 2021 06:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.10_model.r WARNING @ Sat, 03 Apr 2021 06:23:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:23:24: #2 You may need to consider one of the other alternative d(s): 2,12,52 WARNING @ Sat, 03 Apr 2021 06:23:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:23:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:23:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:23:26: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:23:32: 9000000 INFO @ Sat, 03 Apr 2021 06:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.05_summits.bed INFO @ Sat, 03 Apr 2021 06:23:33: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:23:39: 10000000 INFO @ Sat, 03 Apr 2021 06:23:45: 11000000 INFO @ Sat, 03 Apr 2021 06:23:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:23:52: 12000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:23:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.10_summits.bed INFO @ Sat, 03 Apr 2021 06:23:58: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:23:58: 13000000 INFO @ Sat, 03 Apr 2021 06:23:58: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:23:58: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:23:58: #1 total tags in treatment: 13002408 INFO @ Sat, 03 Apr 2021 06:23:58: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:23:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:23:58: #1 tags after filtering in treatment: 13002408 INFO @ Sat, 03 Apr 2021 06:23:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:23:58: #1 finished! INFO @ Sat, 03 Apr 2021 06:23:58: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:23:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:23:59: #2 number of paired peaks: 196 WARNING @ Sat, 03 Apr 2021 06:23:59: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 03 Apr 2021 06:23:59: start model_add_line... INFO @ Sat, 03 Apr 2021 06:23:59: start X-correlation... INFO @ Sat, 03 Apr 2021 06:23:59: end of X-cor INFO @ Sat, 03 Apr 2021 06:23:59: #2 finished! INFO @ Sat, 03 Apr 2021 06:23:59: #2 predicted fragment length is 2 bps INFO @ Sat, 03 Apr 2021 06:23:59: #2 alternative fragment length(s) may be 2,12,52 bps INFO @ Sat, 03 Apr 2021 06:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.20_model.r WARNING @ Sat, 03 Apr 2021 06:23:59: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:23:59: #2 You may need to consider one of the other alternative d(s): 2,12,52 WARNING @ Sat, 03 Apr 2021 06:23:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:23:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:24:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:24:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:24:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:24:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2969571/SRX2969571.20_summits.bed INFO @ Sat, 03 Apr 2021 06:24:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling