Job ID = 6366965 SRX = SRX2576664 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:11:31 prefetch.2.10.7: 1) Downloading 'SRR5272621'... 2020-06-15T23:11:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:46 prefetch.2.10.7: 1) 'SRR5272621' was downloaded successfully Read 22624236 spots for SRR5272621/SRR5272621.sra Written 22624236 spots for SRR5272621/SRR5272621.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: 00:05:13 22624236 reads; of these: 22624236 (100.00%) were unpaired; of these: 895098 (3.96%) aligned 0 times 18042993 (79.75%) aligned exactly 1 time 3686145 (16.29%) aligned >1 times 96.04% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 2785952 / 21729138 = 0.1282 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 08:25:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.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 08:25:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:44: 1000000 INFO @ Tue, 16 Jun 2020 08:25:50: 2000000 INFO @ Tue, 16 Jun 2020 08:25:56: 3000000 INFO @ Tue, 16 Jun 2020 08:26:02: 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 08:26:08: 5000000 INFO @ Tue, 16 Jun 2020 08:26:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.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 08:26:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:14: 6000000 INFO @ Tue, 16 Jun 2020 08:26:15: 1000000 INFO @ Tue, 16 Jun 2020 08:26:21: 7000000 INFO @ Tue, 16 Jun 2020 08:26:22: 2000000 INFO @ Tue, 16 Jun 2020 08:26:28: 8000000 INFO @ Tue, 16 Jun 2020 08:26:29: 3000000 INFO @ Tue, 16 Jun 2020 08:26:35: 9000000 INFO @ Tue, 16 Jun 2020 08:26:36: 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 08:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.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 08:26:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:42: 10000000 INFO @ Tue, 16 Jun 2020 08:26:43: 5000000 INFO @ Tue, 16 Jun 2020 08:26:47: 1000000 INFO @ Tue, 16 Jun 2020 08:26:49: 11000000 INFO @ Tue, 16 Jun 2020 08:26:50: 6000000 INFO @ Tue, 16 Jun 2020 08:26:54: 2000000 INFO @ Tue, 16 Jun 2020 08:26:56: 12000000 INFO @ Tue, 16 Jun 2020 08:26:58: 7000000 INFO @ Tue, 16 Jun 2020 08:27:02: 3000000 INFO @ Tue, 16 Jun 2020 08:27:03: 13000000 INFO @ Tue, 16 Jun 2020 08:27:05: 8000000 INFO @ Tue, 16 Jun 2020 08:27:10: 4000000 INFO @ Tue, 16 Jun 2020 08:27:11: 14000000 INFO @ Tue, 16 Jun 2020 08:27:12: 9000000 INFO @ Tue, 16 Jun 2020 08:27:17: 5000000 INFO @ Tue, 16 Jun 2020 08:27:18: 15000000 INFO @ Tue, 16 Jun 2020 08:27:19: 10000000 INFO @ Tue, 16 Jun 2020 08:27:25: 6000000 INFO @ Tue, 16 Jun 2020 08:27:25: 16000000 INFO @ Tue, 16 Jun 2020 08:27:27: 11000000 INFO @ Tue, 16 Jun 2020 08:27:32: 17000000 INFO @ Tue, 16 Jun 2020 08:27:33: 7000000 INFO @ Tue, 16 Jun 2020 08:27:34: 12000000 INFO @ Tue, 16 Jun 2020 08:27:40: 18000000 INFO @ Tue, 16 Jun 2020 08:27:40: 8000000 INFO @ Tue, 16 Jun 2020 08:27:41: 13000000 INFO @ Tue, 16 Jun 2020 08:27:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:27:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:27:46: #1 total tags in treatment: 18943186 INFO @ Tue, 16 Jun 2020 08:27:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:46: #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 08:27:47: #1 tags after filtering in treatment: 18943186 INFO @ Tue, 16 Jun 2020 08:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:48: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:27:48: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:48: 9000000 INFO @ Tue, 16 Jun 2020 08:27:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:48: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:27:48: #2 alternative fragment length(s) may be 1,46,526,564 bps INFO @ Tue, 16 Jun 2020 08:27:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.05_model.r WARNING @ Tue, 16 Jun 2020 08:27:48: #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 08:27:48: #2 You may need to consider one of the other alternative d(s): 1,46,526,564 WARNING @ Tue, 16 Jun 2020 08:27:48: #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 08:27:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:48: 14000000 INFO @ Tue, 16 Jun 2020 08:27:55: 15000000 INFO @ Tue, 16 Jun 2020 08:27:55: 10000000 INFO @ Tue, 16 Jun 2020 08:28:02: 16000000 INFO @ Tue, 16 Jun 2020 08:28:03: 11000000 INFO @ Tue, 16 Jun 2020 08:28:09: 17000000 INFO @ Tue, 16 Jun 2020 08:28:11: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:16: 18000000 INFO @ Tue, 16 Jun 2020 08:28:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:18: 13000000 INFO @ Tue, 16 Jun 2020 08:28:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:23: #1 total tags in treatment: 18943186 INFO @ Tue, 16 Jun 2020 08:28:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:23: #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 08:28:23: #1 tags after filtering in treatment: 18943186 INFO @ Tue, 16 Jun 2020 08:28:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:24: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:28:24: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:25: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:28:25: #2 alternative fragment length(s) may be 1,46,526,564 bps INFO @ Tue, 16 Jun 2020 08:28:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.10_model.r WARNING @ Tue, 16 Jun 2020 08:28:25: #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 08:28:25: #2 You may need to consider one of the other alternative d(s): 1,46,526,564 WARNING @ Tue, 16 Jun 2020 08:28:25: #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 08:28:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:25: 14000000 INFO @ Tue, 16 Jun 2020 08:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:32: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:32: 15000000 INFO @ Tue, 16 Jun 2020 08:28:39: 16000000 INFO @ Tue, 16 Jun 2020 08:28:46: 17000000 INFO @ Tue, 16 Jun 2020 08:28:53: 18000000 INFO @ Tue, 16 Jun 2020 08:28:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:29:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:29:00: #1 total tags in treatment: 18943186 INFO @ Tue, 16 Jun 2020 08:29:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:00: #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 08:29:00: #1 tags after filtering in treatment: 18943186 INFO @ Tue, 16 Jun 2020 08:29:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:00: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:01: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:29:01: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:01: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:29:01: #2 alternative fragment length(s) may be 1,46,526,564 bps INFO @ Tue, 16 Jun 2020 08:29:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.20_model.r WARNING @ Tue, 16 Jun 2020 08:29:01: #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 08:29:01: #2 You may need to consider one of the other alternative d(s): 1,46,526,564 WARNING @ Tue, 16 Jun 2020 08:29:01: #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 08:29:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:29:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576664/SRX2576664.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling