Job ID = 6368628 SRX = SRX5073496 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:35:31 prefetch.2.10.7: 1) Downloading 'SRR8255716'... 2020-06-16T00:35:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:37:20 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:37:21 prefetch.2.10.7: 'SRR8255716' is valid 2020-06-16T00:37:21 prefetch.2.10.7: 1) 'SRR8255716' was downloaded successfully 2020-06-16T00:37:21 prefetch.2.10.7: 'SRR8255716' has 0 unresolved dependencies Read 27870480 spots for SRR8255716/SRR8255716.sra Written 27870480 spots for SRR8255716/SRR8255716.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: 00:06:38 27870480 reads; of these: 27870480 (100.00%) were unpaired; of these: 403609 (1.45%) aligned 0 times 22573111 (80.99%) aligned exactly 1 time 4893760 (17.56%) aligned >1 times 98.55% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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] 9067409 / 27466871 = 0.3301 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 09:49:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.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 09:49:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:54: 1000000 INFO @ Tue, 16 Jun 2020 09:50:00: 2000000 INFO @ Tue, 16 Jun 2020 09:50:06: 3000000 INFO @ Tue, 16 Jun 2020 09:50:12: 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 09:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.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 09:50:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:18: 5000000 INFO @ Tue, 16 Jun 2020 09:50:25: 1000000 INFO @ Tue, 16 Jun 2020 09:50:25: 6000000 INFO @ Tue, 16 Jun 2020 09:50:32: 2000000 INFO @ Tue, 16 Jun 2020 09:50:32: 7000000 INFO @ Tue, 16 Jun 2020 09:50:39: 3000000 INFO @ Tue, 16 Jun 2020 09:50:39: 8000000 INFO @ Tue, 16 Jun 2020 09:50:45: 4000000 INFO @ Tue, 16 Jun 2020 09:50:45: 9000000 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 09:50:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.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 09:50:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:52: 5000000 INFO @ Tue, 16 Jun 2020 09:50:52: 10000000 INFO @ Tue, 16 Jun 2020 09:50:55: 1000000 INFO @ Tue, 16 Jun 2020 09:50:59: 6000000 INFO @ Tue, 16 Jun 2020 09:50:59: 11000000 INFO @ Tue, 16 Jun 2020 09:51:02: 2000000 INFO @ Tue, 16 Jun 2020 09:51:06: 7000000 INFO @ Tue, 16 Jun 2020 09:51:06: 12000000 INFO @ Tue, 16 Jun 2020 09:51:09: 3000000 INFO @ Tue, 16 Jun 2020 09:51:13: 8000000 INFO @ Tue, 16 Jun 2020 09:51:13: 13000000 INFO @ Tue, 16 Jun 2020 09:51:16: 4000000 INFO @ Tue, 16 Jun 2020 09:51:19: 9000000 INFO @ Tue, 16 Jun 2020 09:51:20: 14000000 INFO @ Tue, 16 Jun 2020 09:51:23: 5000000 INFO @ Tue, 16 Jun 2020 09:51:26: 10000000 INFO @ Tue, 16 Jun 2020 09:51:27: 15000000 INFO @ Tue, 16 Jun 2020 09:51:30: 6000000 INFO @ Tue, 16 Jun 2020 09:51:33: 11000000 INFO @ Tue, 16 Jun 2020 09:51:33: 16000000 INFO @ Tue, 16 Jun 2020 09:51:36: 7000000 INFO @ Tue, 16 Jun 2020 09:51:40: 12000000 INFO @ Tue, 16 Jun 2020 09:51:40: 17000000 INFO @ Tue, 16 Jun 2020 09:51:43: 8000000 INFO @ Tue, 16 Jun 2020 09:51:46: 13000000 INFO @ Tue, 16 Jun 2020 09:51:47: 18000000 INFO @ Tue, 16 Jun 2020 09:51:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:50: #1 total tags in treatment: 18399462 INFO @ Tue, 16 Jun 2020 09:51:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:50: #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 09:51:50: #1 tags after filtering in treatment: 18399462 INFO @ Tue, 16 Jun 2020 09:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:50: 9000000 INFO @ Tue, 16 Jun 2020 09:51:51: #2 number of paired peaks: 221 WARNING @ Tue, 16 Jun 2020 09:51:51: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:52: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:51:52: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 16 Jun 2020 09:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.05_model.r WARNING @ Tue, 16 Jun 2020 09:51:52: #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 09:51:52: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 16 Jun 2020 09:51:52: #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 09:51:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:53: 14000000 INFO @ Tue, 16 Jun 2020 09:51:57: 10000000 INFO @ Tue, 16 Jun 2020 09:52:00: 15000000 INFO @ Tue, 16 Jun 2020 09:52:04: 11000000 INFO @ Tue, 16 Jun 2020 09:52:07: 16000000 INFO @ Tue, 16 Jun 2020 09:52:11: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:14: 17000000 INFO @ Tue, 16 Jun 2020 09:52:18: 13000000 INFO @ Tue, 16 Jun 2020 09:52:21: 18000000 INFO @ Tue, 16 Jun 2020 09:52:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:23: #1 total tags in treatment: 18399462 INFO @ Tue, 16 Jun 2020 09:52:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:23: #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 09:52:23: #1 tags after filtering in treatment: 18399462 INFO @ Tue, 16 Jun 2020 09:52:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:24: 14000000 INFO @ Tue, 16 Jun 2020 09:52:25: #2 number of paired peaks: 221 WARNING @ Tue, 16 Jun 2020 09:52:25: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:25: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:25: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 16 Jun 2020 09:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.10_model.r WARNING @ Tue, 16 Jun 2020 09:52:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:25: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 16 Jun 2020 09:52:25: #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 09:52:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:31: 15000000 INFO @ Tue, 16 Jun 2020 09:52:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:37: 16000000 INFO @ Tue, 16 Jun 2020 09:52:44: 17000000 INFO @ Tue, 16 Jun 2020 09:52:50: 18000000 INFO @ Tue, 16 Jun 2020 09:52:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:53: #1 total tags in treatment: 18399462 INFO @ Tue, 16 Jun 2020 09:52:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:53: #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 09:52:53: #1 tags after filtering in treatment: 18399462 INFO @ Tue, 16 Jun 2020 09:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:54: #2 number of paired peaks: 221 WARNING @ Tue, 16 Jun 2020 09:52:54: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:54: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:54: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 16 Jun 2020 09:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.20_model.r WARNING @ Tue, 16 Jun 2020 09:52:54: #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 09:52:54: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 16 Jun 2020 09:52:54: #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 09:52:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073496/SRX5073496.20_summits.bed INFO @ Tue, 16 Jun 2020 09:53:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling