Job ID = 10166081 SRX = SRX9120612 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: 00:06:11 29658545 reads; of these: 29658545 (100.00%) were unpaired; of these: 1608524 (5.42%) aligned 0 times 23267539 (78.45%) aligned exactly 1 time 4782482 (16.13%) aligned >1 times 94.58% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 6075837 / 28050021 = 0.2166 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 20:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.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 20:40:20: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:40:20: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:40:33: 1000000 INFO @ Thu, 08 Oct 2020 20:40:44: 2000000 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 20:40:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.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 20:40:50: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:40:50: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:40:54: 3000000 INFO @ Thu, 08 Oct 2020 20:40:56: 1000000 INFO @ Thu, 08 Oct 2020 20:41:01: 2000000 INFO @ Thu, 08 Oct 2020 20:41:02: 4000000 INFO @ Thu, 08 Oct 2020 20:41:06: 3000000 INFO @ Thu, 08 Oct 2020 20:41:11: 5000000 INFO @ Thu, 08 Oct 2020 20:41:12: 4000000 INFO @ Thu, 08 Oct 2020 20:41:17: 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 @ Thu, 08 Oct 2020 20:41:19: 6000000 INFO @ Thu, 08 Oct 2020 20:41:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.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 20:41:20: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:20: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:22: 6000000 INFO @ Thu, 08 Oct 2020 20:41:26: 7000000 INFO @ Thu, 08 Oct 2020 20:41:28: 1000000 INFO @ Thu, 08 Oct 2020 20:41:28: 7000000 INFO @ Thu, 08 Oct 2020 20:41:33: 8000000 INFO @ Thu, 08 Oct 2020 20:41:33: 8000000 INFO @ Thu, 08 Oct 2020 20:41:34: 2000000 INFO @ Thu, 08 Oct 2020 20:41:39: 9000000 INFO @ Thu, 08 Oct 2020 20:41:39: 9000000 INFO @ Thu, 08 Oct 2020 20:41:40: 3000000 INFO @ Thu, 08 Oct 2020 20:41:45: 10000000 INFO @ Thu, 08 Oct 2020 20:41:45: 10000000 INFO @ Thu, 08 Oct 2020 20:41:46: 4000000 INFO @ Thu, 08 Oct 2020 20:41:51: 11000000 INFO @ Thu, 08 Oct 2020 20:41:51: 11000000 INFO @ Thu, 08 Oct 2020 20:41:51: 5000000 INFO @ Thu, 08 Oct 2020 20:41:56: 12000000 INFO @ Thu, 08 Oct 2020 20:41:57: 6000000 INFO @ Thu, 08 Oct 2020 20:41:57: 12000000 INFO @ Thu, 08 Oct 2020 20:42:02: 13000000 INFO @ Thu, 08 Oct 2020 20:42:03: 7000000 INFO @ Thu, 08 Oct 2020 20:42:03: 13000000 INFO @ Thu, 08 Oct 2020 20:42:08: 14000000 INFO @ Thu, 08 Oct 2020 20:42:08: 8000000 INFO @ Thu, 08 Oct 2020 20:42:09: 14000000 INFO @ Thu, 08 Oct 2020 20:42:14: 15000000 INFO @ Thu, 08 Oct 2020 20:42:14: 9000000 INFO @ Thu, 08 Oct 2020 20:42:15: 15000000 INFO @ Thu, 08 Oct 2020 20:42:19: 16000000 INFO @ Thu, 08 Oct 2020 20:42:20: 10000000 INFO @ Thu, 08 Oct 2020 20:42:20: 16000000 INFO @ Thu, 08 Oct 2020 20:42:25: 17000000 INFO @ Thu, 08 Oct 2020 20:42:25: 11000000 INFO @ Thu, 08 Oct 2020 20:42:26: 17000000 INFO @ Thu, 08 Oct 2020 20:42:31: 18000000 INFO @ Thu, 08 Oct 2020 20:42:31: 12000000 INFO @ Thu, 08 Oct 2020 20:42:32: 18000000 INFO @ Thu, 08 Oct 2020 20:42:36: 19000000 INFO @ Thu, 08 Oct 2020 20:42:37: 13000000 INFO @ Thu, 08 Oct 2020 20:42:37: 19000000 INFO @ Thu, 08 Oct 2020 20:42:42: 20000000 INFO @ Thu, 08 Oct 2020 20:42:42: 14000000 INFO @ Thu, 08 Oct 2020 20:42:43: 20000000 INFO @ Thu, 08 Oct 2020 20:42:48: 21000000 INFO @ Thu, 08 Oct 2020 20:42:48: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:42:49: 21000000 INFO @ Thu, 08 Oct 2020 20:42:54: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:42:54: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:42:54: #1 total tags in treatment: 21974184 INFO @ Thu, 08 Oct 2020 20:42:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:42:54: #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 20:42:54: 16000000 INFO @ Thu, 08 Oct 2020 20:42:54: #1 tags after filtering in treatment: 21974184 INFO @ Thu, 08 Oct 2020 20:42:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:42:54: #1 finished! INFO @ Thu, 08 Oct 2020 20:42:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:42:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:42:54: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:42:54: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:42:54: #1 total tags in treatment: 21974184 INFO @ Thu, 08 Oct 2020 20:42:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:42:54: #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 20:42:55: #1 tags after filtering in treatment: 21974184 INFO @ Thu, 08 Oct 2020 20:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:42:55: #1 finished! INFO @ Thu, 08 Oct 2020 20:42:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:42:55: #2 number of paired peaks: 193 WARNING @ Thu, 08 Oct 2020 20:42:55: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Thu, 08 Oct 2020 20:42:55: start model_add_line... INFO @ Thu, 08 Oct 2020 20:42:55: start X-correlation... INFO @ Thu, 08 Oct 2020 20:42:55: end of X-cor INFO @ Thu, 08 Oct 2020 20:42:55: #2 finished! INFO @ Thu, 08 Oct 2020 20:42:55: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:42:55: #2 alternative fragment length(s) may be 1,39,500,533 bps INFO @ Thu, 08 Oct 2020 20:42:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.05_model.r WARNING @ Thu, 08 Oct 2020 20:42:55: #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 20:42:55: #2 You may need to consider one of the other alternative d(s): 1,39,500,533 WARNING @ Thu, 08 Oct 2020 20:42:55: #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 20:42:55: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:42:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:42:56: #2 number of paired peaks: 193 WARNING @ Thu, 08 Oct 2020 20:42:56: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Thu, 08 Oct 2020 20:42:56: start model_add_line... INFO @ Thu, 08 Oct 2020 20:42:56: start X-correlation... INFO @ Thu, 08 Oct 2020 20:42:56: end of X-cor INFO @ Thu, 08 Oct 2020 20:42:56: #2 finished! INFO @ Thu, 08 Oct 2020 20:42:56: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:42:56: #2 alternative fragment length(s) may be 1,39,500,533 bps INFO @ Thu, 08 Oct 2020 20:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.10_model.r WARNING @ Thu, 08 Oct 2020 20:42:56: #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 20:42:56: #2 You may need to consider one of the other alternative d(s): 1,39,500,533 WARNING @ Thu, 08 Oct 2020 20:42:56: #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 20:42:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:42:59: 17000000 INFO @ Thu, 08 Oct 2020 20:43:04: 18000000 INFO @ Thu, 08 Oct 2020 20:43:09: 19000000 INFO @ Thu, 08 Oct 2020 20:43:14: 20000000 INFO @ Thu, 08 Oct 2020 20:43:20: 21000000 INFO @ Thu, 08 Oct 2020 20:43:25: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:43:25: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:43:25: #1 total tags in treatment: 21974184 INFO @ Thu, 08 Oct 2020 20:43:25: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:25: #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 20:43:25: #1 tags after filtering in treatment: 21974184 INFO @ Thu, 08 Oct 2020 20:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:25: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:25: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:26: #2 number of paired peaks: 193 WARNING @ Thu, 08 Oct 2020 20:43:26: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Thu, 08 Oct 2020 20:43:26: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:26: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:26: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:26: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:26: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:26: #2 alternative fragment length(s) may be 1,39,500,533 bps INFO @ Thu, 08 Oct 2020 20:43:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.20_model.r WARNING @ Thu, 08 Oct 2020 20:43:26: #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 20:43:26: #2 You may need to consider one of the other alternative d(s): 1,39,500,533 WARNING @ Thu, 08 Oct 2020 20:43:26: #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 20:43:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:43:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:43:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.05_summits.bed INFO @ Thu, 08 Oct 2020 20:43:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.10_summits.bed INFO @ Thu, 08 Oct 2020 20:43:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:44:01: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:44:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120612/SRX9120612.20_summits.bed INFO @ Thu, 08 Oct 2020 20:44:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling