Job ID = 10166077 SRX = SRX9120615 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: 00:00:00 Multiseed full-index search: 00:04:30 22488133 reads; of these: 22488133 (100.00%) were unpaired; of these: 712449 (3.17%) aligned 0 times 18191071 (80.89%) aligned exactly 1 time 3584613 (15.94%) aligned >1 times 96.83% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 3064742 / 21775684 = 0.1407 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 @ Thu, 08 Oct 2020 20:37:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.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 @ Thu, 08 Oct 2020 20:37:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:37:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:37:22: 1000000 INFO @ Thu, 08 Oct 2020 20:37:27: 2000000 INFO @ Thu, 08 Oct 2020 20:37:33: 3000000 INFO @ Thu, 08 Oct 2020 20:37:38: 4000000 INFO @ Thu, 08 Oct 2020 20:37:43: 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 @ Thu, 08 Oct 2020 20:37:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.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 @ Thu, 08 Oct 2020 20:37:46: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:37:46: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:37:49: 6000000 INFO @ Thu, 08 Oct 2020 20:37:53: 1000000 INFO @ Thu, 08 Oct 2020 20:37:55: 7000000 INFO @ Thu, 08 Oct 2020 20:38:00: 2000000 INFO @ Thu, 08 Oct 2020 20:38:01: 8000000 INFO @ Thu, 08 Oct 2020 20:38:06: 3000000 INFO @ Thu, 08 Oct 2020 20:38:08: 9000000 INFO @ Thu, 08 Oct 2020 20:38:13: 4000000 INFO @ Thu, 08 Oct 2020 20:38:14: 10000000 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 @ Thu, 08 Oct 2020 20:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.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 @ Thu, 08 Oct 2020 20:38:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:38:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:38:20: 5000000 INFO @ Thu, 08 Oct 2020 20:38:20: 11000000 INFO @ Thu, 08 Oct 2020 20:38:23: 1000000 INFO @ Thu, 08 Oct 2020 20:38:27: 12000000 INFO @ Thu, 08 Oct 2020 20:38:27: 6000000 INFO @ Thu, 08 Oct 2020 20:38:29: 2000000 INFO @ Thu, 08 Oct 2020 20:38:33: 13000000 INFO @ Thu, 08 Oct 2020 20:38:34: 7000000 INFO @ Thu, 08 Oct 2020 20:38:36: 3000000 INFO @ Thu, 08 Oct 2020 20:38:40: 14000000 INFO @ Thu, 08 Oct 2020 20:38:41: 8000000 INFO @ Thu, 08 Oct 2020 20:38:43: 4000000 INFO @ Thu, 08 Oct 2020 20:38:46: 15000000 INFO @ Thu, 08 Oct 2020 20:38:48: 9000000 INFO @ Thu, 08 Oct 2020 20:38:49: 5000000 INFO @ Thu, 08 Oct 2020 20:38:52: 16000000 INFO @ Thu, 08 Oct 2020 20:38:55: 10000000 INFO @ Thu, 08 Oct 2020 20:38:56: 6000000 INFO @ Thu, 08 Oct 2020 20:38:59: 17000000 INFO @ Thu, 08 Oct 2020 20:39:02: 11000000 INFO @ Thu, 08 Oct 2020 20:39:03: 7000000 INFO @ Thu, 08 Oct 2020 20:39:05: 18000000 INFO @ Thu, 08 Oct 2020 20:39:09: 12000000 INFO @ Thu, 08 Oct 2020 20:39:10: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:39:10: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:39:10: #1 total tags in treatment: 18710942 INFO @ Thu, 08 Oct 2020 20:39:10: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:39:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:39:10: #1 tags after filtering in treatment: 18710942 INFO @ Thu, 08 Oct 2020 20:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:39:10: #1 finished! INFO @ Thu, 08 Oct 2020 20:39:10: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:39:10: 8000000 INFO @ Thu, 08 Oct 2020 20:39:11: #2 number of paired peaks: 205 WARNING @ Thu, 08 Oct 2020 20:39:11: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Thu, 08 Oct 2020 20:39:11: start model_add_line... INFO @ Thu, 08 Oct 2020 20:39:12: start X-correlation... INFO @ Thu, 08 Oct 2020 20:39:12: end of X-cor INFO @ Thu, 08 Oct 2020 20:39:12: #2 finished! INFO @ Thu, 08 Oct 2020 20:39:12: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:39:12: #2 alternative fragment length(s) may be 1,14,38,46,537 bps INFO @ Thu, 08 Oct 2020 20:39:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05_model.r WARNING @ Thu, 08 Oct 2020 20:39:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:39:12: #2 You may need to consider one of the other alternative d(s): 1,14,38,46,537 WARNING @ Thu, 08 Oct 2020 20:39:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:39:12: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:39:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:39:16: 13000000 INFO @ Thu, 08 Oct 2020 20:39:17: 9000000 INFO @ Thu, 08 Oct 2020 20:39:23: 14000000 INFO @ Thu, 08 Oct 2020 20:39:24: 10000000 INFO @ Thu, 08 Oct 2020 20:39:30: 15000000 INFO @ Thu, 08 Oct 2020 20:39:31: 11000000 INFO @ Thu, 08 Oct 2020 20:39:37: 16000000 INFO @ Thu, 08 Oct 2020 20:39:37: 12000000 INFO @ Thu, 08 Oct 2020 20:39:42: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:39:44: 17000000 INFO @ Thu, 08 Oct 2020 20:39:44: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:39:51: 18000000 INFO @ Thu, 08 Oct 2020 20:39:52: 14000000 INFO @ Thu, 08 Oct 2020 20:39:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:39:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:39:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.05_summits.bed INFO @ Thu, 08 Oct 2020 20:39:56: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:39:56: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:39:56: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:39:56: #1 total tags in treatment: 18710942 INFO @ Thu, 08 Oct 2020 20:39:56: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:39:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:39:56: #1 tags after filtering in treatment: 18710942 INFO @ Thu, 08 Oct 2020 20:39:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:39:56: #1 finished! INFO @ Thu, 08 Oct 2020 20:39:56: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:39:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:39:58: #2 number of paired peaks: 205 WARNING @ Thu, 08 Oct 2020 20:39:58: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Thu, 08 Oct 2020 20:39:58: start model_add_line... INFO @ Thu, 08 Oct 2020 20:39:58: start X-correlation... INFO @ Thu, 08 Oct 2020 20:39:58: end of X-cor INFO @ Thu, 08 Oct 2020 20:39:58: #2 finished! INFO @ Thu, 08 Oct 2020 20:39:58: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:39:58: #2 alternative fragment length(s) may be 1,14,38,46,537 bps INFO @ Thu, 08 Oct 2020 20:39:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10_model.r WARNING @ Thu, 08 Oct 2020 20:39:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:39:58: #2 You may need to consider one of the other alternative d(s): 1,14,38,46,537 WARNING @ Thu, 08 Oct 2020 20:39:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:39:58: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:39:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:39:59: 15000000 INFO @ Thu, 08 Oct 2020 20:40:05: 16000000 INFO @ Thu, 08 Oct 2020 20:40:12: 17000000 INFO @ Thu, 08 Oct 2020 20:40:19: 18000000 INFO @ Thu, 08 Oct 2020 20:40:23: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:40:23: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:40:23: #1 total tags in treatment: 18710942 INFO @ Thu, 08 Oct 2020 20:40:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:40:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:40:23: #1 tags after filtering in treatment: 18710942 INFO @ Thu, 08 Oct 2020 20:40:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:40:23: #1 finished! INFO @ Thu, 08 Oct 2020 20:40:23: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:40:25: #2 number of paired peaks: 205 WARNING @ Thu, 08 Oct 2020 20:40:25: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Thu, 08 Oct 2020 20:40:25: start model_add_line... INFO @ Thu, 08 Oct 2020 20:40:25: start X-correlation... INFO @ Thu, 08 Oct 2020 20:40:25: end of X-cor INFO @ Thu, 08 Oct 2020 20:40:25: #2 finished! INFO @ Thu, 08 Oct 2020 20:40:25: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:40:25: #2 alternative fragment length(s) may be 1,14,38,46,537 bps INFO @ Thu, 08 Oct 2020 20:40:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20_model.r WARNING @ Thu, 08 Oct 2020 20:40:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:40:25: #2 You may need to consider one of the other alternative d(s): 1,14,38,46,537 WARNING @ Thu, 08 Oct 2020 20:40:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:40:25: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:40:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:40:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:40:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:40:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:40:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.10_summits.bed INFO @ Thu, 08 Oct 2020 20:40:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:40:55: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:41:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:41:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:41:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120615/SRX9120615.20_summits.bed INFO @ Thu, 08 Oct 2020 20:41:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling