Job ID = 6529094 SRX = SRX059224 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: 00:03:56 19829939 reads; of these: 19829939 (100.00%) were unpaired; of these: 237055 (1.20%) aligned 0 times 15862957 (79.99%) aligned exactly 1 time 3729927 (18.81%) aligned >1 times 98.80% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 2727264 / 19592884 = 0.1392 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 @ Tue, 30 Jun 2020 01:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.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 @ Tue, 30 Jun 2020 01:28:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:28:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:01: 1000000 INFO @ Tue, 30 Jun 2020 01:29:07: 2000000 INFO @ Tue, 30 Jun 2020 01:29:13: 3000000 INFO @ Tue, 30 Jun 2020 01:29:19: 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 @ Tue, 30 Jun 2020 01:29:25: 5000000 INFO @ Tue, 30 Jun 2020 01:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.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 @ Tue, 30 Jun 2020 01:29:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:31: 6000000 INFO @ Tue, 30 Jun 2020 01:29:31: 1000000 INFO @ Tue, 30 Jun 2020 01:29:37: 7000000 INFO @ Tue, 30 Jun 2020 01:29:38: 2000000 INFO @ Tue, 30 Jun 2020 01:29:43: 8000000 INFO @ Tue, 30 Jun 2020 01:29:44: 3000000 INFO @ Tue, 30 Jun 2020 01:29:49: 9000000 INFO @ Tue, 30 Jun 2020 01:29:50: 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 @ Tue, 30 Jun 2020 01:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.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 @ Tue, 30 Jun 2020 01:29:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:56: 10000000 INFO @ Tue, 30 Jun 2020 01:29:56: 5000000 INFO @ Tue, 30 Jun 2020 01:30:02: 11000000 INFO @ Tue, 30 Jun 2020 01:30:03: 1000000 INFO @ Tue, 30 Jun 2020 01:30:03: 6000000 INFO @ Tue, 30 Jun 2020 01:30:09: 12000000 INFO @ Tue, 30 Jun 2020 01:30:09: 7000000 INFO @ Tue, 30 Jun 2020 01:30:10: 2000000 INFO @ Tue, 30 Jun 2020 01:30:16: 13000000 INFO @ Tue, 30 Jun 2020 01:30:16: 8000000 INFO @ Tue, 30 Jun 2020 01:30:17: 3000000 INFO @ Tue, 30 Jun 2020 01:30:22: 14000000 INFO @ Tue, 30 Jun 2020 01:30:23: 9000000 INFO @ Tue, 30 Jun 2020 01:30:25: 4000000 INFO @ Tue, 30 Jun 2020 01:30:29: 15000000 INFO @ Tue, 30 Jun 2020 01:30:29: 10000000 INFO @ Tue, 30 Jun 2020 01:30:32: 5000000 INFO @ Tue, 30 Jun 2020 01:30:35: 16000000 INFO @ Tue, 30 Jun 2020 01:30:36: 11000000 INFO @ Tue, 30 Jun 2020 01:30:39: 6000000 INFO @ Tue, 30 Jun 2020 01:30:41: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:30:41: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:30:41: #1 total tags in treatment: 16865620 INFO @ Tue, 30 Jun 2020 01:30:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:30:41: #1 tags after filtering in treatment: 16865620 INFO @ Tue, 30 Jun 2020 01:30:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:41: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:42: 12000000 INFO @ Tue, 30 Jun 2020 01:30:43: #2 number of paired peaks: 181 WARNING @ Tue, 30 Jun 2020 01:30:43: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:43: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:43: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:43: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:43: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:43: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:30:43: #2 alternative fragment length(s) may be 1,32,529,598 bps INFO @ Tue, 30 Jun 2020 01:30:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.05_model.r WARNING @ Tue, 30 Jun 2020 01:30:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:30:43: #2 You may need to consider one of the other alternative d(s): 1,32,529,598 WARNING @ Tue, 30 Jun 2020 01:30:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:30:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:30:46: 7000000 INFO @ Tue, 30 Jun 2020 01:30:49: 13000000 INFO @ Tue, 30 Jun 2020 01:30:53: 8000000 INFO @ Tue, 30 Jun 2020 01:30:55: 14000000 INFO @ Tue, 30 Jun 2020 01:31:01: 9000000 INFO @ Tue, 30 Jun 2020 01:31:02: 15000000 INFO @ Tue, 30 Jun 2020 01:31:08: 10000000 INFO @ Tue, 30 Jun 2020 01:31:09: 16000000 INFO @ Tue, 30 Jun 2020 01:31:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:31:14: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:31:14: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:31:14: #1 total tags in treatment: 16865620 INFO @ Tue, 30 Jun 2020 01:31:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:31:15: #1 tags after filtering in treatment: 16865620 INFO @ Tue, 30 Jun 2020 01:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:31:15: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:15: 11000000 INFO @ Tue, 30 Jun 2020 01:31:16: #2 number of paired peaks: 181 WARNING @ Tue, 30 Jun 2020 01:31:16: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 30 Jun 2020 01:31:16: start model_add_line... INFO @ Tue, 30 Jun 2020 01:31:16: start X-correlation... INFO @ Tue, 30 Jun 2020 01:31:16: end of X-cor INFO @ Tue, 30 Jun 2020 01:31:16: #2 finished! INFO @ Tue, 30 Jun 2020 01:31:16: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:31:16: #2 alternative fragment length(s) may be 1,32,529,598 bps INFO @ Tue, 30 Jun 2020 01:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.10_model.r WARNING @ Tue, 30 Jun 2020 01:31:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:31:16: #2 You may need to consider one of the other alternative d(s): 1,32,529,598 WARNING @ Tue, 30 Jun 2020 01:31:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:31:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:31:22: 12000000 INFO @ Tue, 30 Jun 2020 01:31:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.05_summits.bed INFO @ Tue, 30 Jun 2020 01:31:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:31:29: 13000000 INFO @ Tue, 30 Jun 2020 01:31:35: 14000000 INFO @ Tue, 30 Jun 2020 01:31:42: 15000000 INFO @ Tue, 30 Jun 2020 01:31:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:31:49: 16000000 INFO @ Tue, 30 Jun 2020 01:31:55: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:31:55: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:31:55: #1 total tags in treatment: 16865620 INFO @ Tue, 30 Jun 2020 01:31:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:31:55: #1 tags after filtering in treatment: 16865620 INFO @ Tue, 30 Jun 2020 01:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:31:55: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:55: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:31:56: #2 number of paired peaks: 181 WARNING @ Tue, 30 Jun 2020 01:31:56: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 30 Jun 2020 01:31:56: start model_add_line... INFO @ Tue, 30 Jun 2020 01:31:57: start X-correlation... INFO @ Tue, 30 Jun 2020 01:31:57: end of X-cor INFO @ Tue, 30 Jun 2020 01:31:57: #2 finished! INFO @ Tue, 30 Jun 2020 01:31:57: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:31:57: #2 alternative fragment length(s) may be 1,32,529,598 bps INFO @ Tue, 30 Jun 2020 01:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.20_model.r WARNING @ Tue, 30 Jun 2020 01:31:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:31:57: #2 You may need to consider one of the other alternative d(s): 1,32,529,598 WARNING @ Tue, 30 Jun 2020 01:31:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:31:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:32:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:32:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:32:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.10_summits.bed INFO @ Tue, 30 Jun 2020 01:32:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:32:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:32:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:32:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:32:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059224/SRX059224.20_summits.bed INFO @ Tue, 30 Jun 2020 01:32:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling