Job ID = 6368682 SRX = SRX5402709 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:01 prefetch.2.10.7: 1) Downloading 'SRR8602943'... 2020-06-16T00:29:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:56 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:56 prefetch.2.10.7: 1) 'SRR8602943' was downloaded successfully Read 40110722 spots for SRR8602943/SRR8602943.sra Written 40110722 spots for SRR8602943/SRR8602943.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: 00:07:34 40110722 reads; of these: 40110722 (100.00%) were unpaired; of these: 8305598 (20.71%) aligned 0 times 26345360 (65.68%) aligned exactly 1 time 5459764 (13.61%) aligned >1 times 79.29% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 7373068 / 31805124 = 0.2318 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, 16 Jun 2020 09:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.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, 16 Jun 2020 09:49:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:37: 1000000 INFO @ Tue, 16 Jun 2020 09:49:43: 2000000 INFO @ Tue, 16 Jun 2020 09:49:49: 3000000 INFO @ Tue, 16 Jun 2020 09:49:55: 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, 16 Jun 2020 09:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.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, 16 Jun 2020 09:50:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:02: 5000000 INFO @ Tue, 16 Jun 2020 09:50:06: 1000000 INFO @ Tue, 16 Jun 2020 09:50:09: 6000000 INFO @ Tue, 16 Jun 2020 09:50:12: 2000000 INFO @ Tue, 16 Jun 2020 09:50:16: 7000000 INFO @ Tue, 16 Jun 2020 09:50:18: 3000000 INFO @ Tue, 16 Jun 2020 09:50:23: 8000000 INFO @ Tue, 16 Jun 2020 09:50:24: 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, 16 Jun 2020 09:50:30: 9000000 INFO @ Tue, 16 Jun 2020 09:50:30: 5000000 INFO @ Tue, 16 Jun 2020 09:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.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, 16 Jun 2020 09:50:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:36: 6000000 INFO @ Tue, 16 Jun 2020 09:50:37: 1000000 INFO @ Tue, 16 Jun 2020 09:50:37: 10000000 INFO @ Tue, 16 Jun 2020 09:50:43: 7000000 INFO @ Tue, 16 Jun 2020 09:50:43: 2000000 INFO @ Tue, 16 Jun 2020 09:50:44: 11000000 INFO @ Tue, 16 Jun 2020 09:50:49: 8000000 INFO @ Tue, 16 Jun 2020 09:50:49: 3000000 INFO @ Tue, 16 Jun 2020 09:50:51: 12000000 INFO @ Tue, 16 Jun 2020 09:50:55: 9000000 INFO @ Tue, 16 Jun 2020 09:50:55: 4000000 INFO @ Tue, 16 Jun 2020 09:50:58: 13000000 INFO @ Tue, 16 Jun 2020 09:51:01: 10000000 INFO @ Tue, 16 Jun 2020 09:51:01: 5000000 INFO @ Tue, 16 Jun 2020 09:51:05: 14000000 INFO @ Tue, 16 Jun 2020 09:51:07: 11000000 INFO @ Tue, 16 Jun 2020 09:51:07: 6000000 INFO @ Tue, 16 Jun 2020 09:51:11: 15000000 INFO @ Tue, 16 Jun 2020 09:51:13: 12000000 INFO @ Tue, 16 Jun 2020 09:51:13: 7000000 INFO @ Tue, 16 Jun 2020 09:51:18: 16000000 INFO @ Tue, 16 Jun 2020 09:51:19: 13000000 INFO @ Tue, 16 Jun 2020 09:51:19: 8000000 INFO @ Tue, 16 Jun 2020 09:51:25: 14000000 INFO @ Tue, 16 Jun 2020 09:51:25: 17000000 INFO @ Tue, 16 Jun 2020 09:51:26: 9000000 INFO @ Tue, 16 Jun 2020 09:51:31: 15000000 INFO @ Tue, 16 Jun 2020 09:51:31: 10000000 INFO @ Tue, 16 Jun 2020 09:51:32: 18000000 INFO @ Tue, 16 Jun 2020 09:51:37: 16000000 INFO @ Tue, 16 Jun 2020 09:51:37: 11000000 INFO @ Tue, 16 Jun 2020 09:51:39: 19000000 INFO @ Tue, 16 Jun 2020 09:51:43: 17000000 INFO @ Tue, 16 Jun 2020 09:51:43: 12000000 INFO @ Tue, 16 Jun 2020 09:51:45: 20000000 INFO @ Tue, 16 Jun 2020 09:51:49: 18000000 INFO @ Tue, 16 Jun 2020 09:51:49: 13000000 INFO @ Tue, 16 Jun 2020 09:51:52: 21000000 INFO @ Tue, 16 Jun 2020 09:51:55: 19000000 INFO @ Tue, 16 Jun 2020 09:51:55: 14000000 INFO @ Tue, 16 Jun 2020 09:51:58: 22000000 INFO @ Tue, 16 Jun 2020 09:52:00: 20000000 INFO @ Tue, 16 Jun 2020 09:52:01: 15000000 INFO @ Tue, 16 Jun 2020 09:52:04: 23000000 INFO @ Tue, 16 Jun 2020 09:52:06: 21000000 INFO @ Tue, 16 Jun 2020 09:52:07: 16000000 INFO @ Tue, 16 Jun 2020 09:52:11: 24000000 INFO @ Tue, 16 Jun 2020 09:52:12: 22000000 INFO @ Tue, 16 Jun 2020 09:52:13: 17000000 INFO @ Tue, 16 Jun 2020 09:52:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:14: #1 total tags in treatment: 24432056 INFO @ Tue, 16 Jun 2020 09:52:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:52:14: #1 tags after filtering in treatment: 24432056 INFO @ Tue, 16 Jun 2020 09:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:15: #2 number of paired peaks: 152 WARNING @ Tue, 16 Jun 2020 09:52:15: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:16: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:16: #2 alternative fragment length(s) may be 1,11,17 bps INFO @ Tue, 16 Jun 2020 09:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.05_model.r WARNING @ Tue, 16 Jun 2020 09:52:16: #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, 16 Jun 2020 09:52:16: #2 You may need to consider one of the other alternative d(s): 1,11,17 WARNING @ Tue, 16 Jun 2020 09:52:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:52:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:18: 23000000 INFO @ Tue, 16 Jun 2020 09:52:19: 18000000 INFO @ Tue, 16 Jun 2020 09:52:24: 24000000 INFO @ Tue, 16 Jun 2020 09:52:25: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:26: #1 total tags in treatment: 24432056 INFO @ Tue, 16 Jun 2020 09:52:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:52:27: #1 tags after filtering in treatment: 24432056 INFO @ Tue, 16 Jun 2020 09:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:28: #2 number of paired peaks: 152 WARNING @ Tue, 16 Jun 2020 09:52:28: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:29: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:29: #2 alternative fragment length(s) may be 1,11,17 bps INFO @ Tue, 16 Jun 2020 09:52:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.10_model.r WARNING @ Tue, 16 Jun 2020 09:52:29: #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, 16 Jun 2020 09:52:29: #2 You may need to consider one of the other alternative d(s): 1,11,17 WARNING @ Tue, 16 Jun 2020 09:52:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:52:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:31: 20000000 INFO @ Tue, 16 Jun 2020 09:52:36: 21000000 INFO @ Tue, 16 Jun 2020 09:52:41: 22000000 INFO @ Tue, 16 Jun 2020 09:52:46: 23000000 INFO @ Tue, 16 Jun 2020 09:52:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:52: 24000000 INFO @ Tue, 16 Jun 2020 09:52:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:54: #1 total tags in treatment: 24432056 INFO @ Tue, 16 Jun 2020 09:52:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:52:55: #1 tags after filtering in treatment: 24432056 INFO @ Tue, 16 Jun 2020 09:52:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:56: #2 number of paired peaks: 152 WARNING @ Tue, 16 Jun 2020 09:52:56: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:56: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:56: #2 alternative fragment length(s) may be 1,11,17 bps INFO @ Tue, 16 Jun 2020 09:52:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.20_model.r WARNING @ Tue, 16 Jun 2020 09:52:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:56: #2 You may need to consider one of the other alternative d(s): 1,11,17 WARNING @ Tue, 16 Jun 2020 09:52:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:52:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:06: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402709/SRX5402709.20_summits.bed INFO @ Tue, 16 Jun 2020 09:53:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling