Job ID = 6527400 SRX = SRX059224 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:30:04 prefetch.2.10.7: 1) Downloading 'SRR190664'... 2020-06-29T12:30:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:33:50 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:33:50 prefetch.2.10.7: 1) 'SRR190664' was downloaded successfully Read 19829939 spots for SRR190664/SRR190664.sra Written 19829939 spots for SRR190664/SRR190664.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: 00:00:01 Multiseed full-index search: 00:03:35 19829939 reads; of these: 19829939 (100.00%) were unpaired; of these: 238332 (1.20%) aligned 0 times 15861889 (79.99%) aligned exactly 1 time 3729718 (18.81%) aligned >1 times 98.80% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 2727171 / 19591607 = 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 @ Mon, 29 Jun 2020 21:47:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 @ Mon, 29 Jun 2020 21:47:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:47:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:47:14: 1000000 INFO @ Mon, 29 Jun 2020 21:47:19: 2000000 INFO @ Mon, 29 Jun 2020 21:47:25: 3000000 INFO @ Mon, 29 Jun 2020 21:47:30: 4000000 INFO @ Mon, 29 Jun 2020 21:47:35: 5000000 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 @ Mon, 29 Jun 2020 21:47:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 @ Mon, 29 Jun 2020 21:47:39: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:47:39: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:47:40: 6000000 INFO @ Mon, 29 Jun 2020 21:47:44: 1000000 INFO @ Mon, 29 Jun 2020 21:47:46: 7000000 INFO @ Mon, 29 Jun 2020 21:47:50: 2000000 INFO @ Mon, 29 Jun 2020 21:47:52: 8000000 INFO @ Mon, 29 Jun 2020 21:47:56: 3000000 INFO @ Mon, 29 Jun 2020 21:47:57: 9000000 INFO @ Mon, 29 Jun 2020 21:48:02: 4000000 INFO @ Mon, 29 Jun 2020 21:48:03: 10000000 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 @ Mon, 29 Jun 2020 21:48:07: 5000000 INFO @ Mon, 29 Jun 2020 21:48:09: 11000000 INFO @ Mon, 29 Jun 2020 21:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 @ Mon, 29 Jun 2020 21:48:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:48:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:48:13: 6000000 INFO @ Mon, 29 Jun 2020 21:48:14: 12000000 INFO @ Mon, 29 Jun 2020 21:48:15: 1000000 INFO @ Mon, 29 Jun 2020 21:48:19: 7000000 INFO @ Mon, 29 Jun 2020 21:48:20: 13000000 INFO @ Mon, 29 Jun 2020 21:48:21: 2000000 INFO @ Mon, 29 Jun 2020 21:48:25: 8000000 INFO @ Mon, 29 Jun 2020 21:48:26: 14000000 INFO @ Mon, 29 Jun 2020 21:48:26: 3000000 INFO @ Mon, 29 Jun 2020 21:48:31: 9000000 INFO @ Mon, 29 Jun 2020 21:48:32: 15000000 INFO @ Mon, 29 Jun 2020 21:48:32: 4000000 INFO @ Mon, 29 Jun 2020 21:48:37: 10000000 INFO @ Mon, 29 Jun 2020 21:48:37: 16000000 INFO @ Mon, 29 Jun 2020 21:48:38: 5000000 INFO @ Mon, 29 Jun 2020 21:48:42: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 21:48:42: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 21:48:42: #1 total tags in treatment: 16864436 INFO @ Mon, 29 Jun 2020 21:48:42: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:48:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:48:43: #1 tags after filtering in treatment: 16864436 INFO @ Mon, 29 Jun 2020 21:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:48:43: #1 finished! INFO @ Mon, 29 Jun 2020 21:48:43: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:48:43: 11000000 INFO @ Mon, 29 Jun 2020 21:48:44: 6000000 INFO @ Mon, 29 Jun 2020 21:48:44: #2 number of paired peaks: 181 WARNING @ Mon, 29 Jun 2020 21:48:44: 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 @ Mon, 29 Jun 2020 21:48:44: start model_add_line... INFO @ Mon, 29 Jun 2020 21:48:44: start X-correlation... INFO @ Mon, 29 Jun 2020 21:48:44: end of X-cor INFO @ Mon, 29 Jun 2020 21:48:44: #2 finished! INFO @ Mon, 29 Jun 2020 21:48:44: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 21:48:44: #2 alternative fragment length(s) may be 1,33,529,598 bps INFO @ Mon, 29 Jun 2020 21:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.05_model.r WARNING @ Mon, 29 Jun 2020 21:48:44: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:48:44: #2 You may need to consider one of the other alternative d(s): 1,33,529,598 WARNING @ Mon, 29 Jun 2020 21:48:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:48:44: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:48:49: 12000000 INFO @ Mon, 29 Jun 2020 21:48:49: 7000000 INFO @ Mon, 29 Jun 2020 21:48:54: 13000000 INFO @ Mon, 29 Jun 2020 21:48:55: 8000000 INFO @ Mon, 29 Jun 2020 21:49:00: 14000000 INFO @ Mon, 29 Jun 2020 21:49:01: 9000000 INFO @ Mon, 29 Jun 2020 21:49:06: 10000000 INFO @ Mon, 29 Jun 2020 21:49:06: 15000000 INFO @ Mon, 29 Jun 2020 21:49:12: 11000000 INFO @ Mon, 29 Jun 2020 21:49:12: 16000000 INFO @ Mon, 29 Jun 2020 21:49:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:49:17: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 21:49:17: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 21:49:17: #1 total tags in treatment: 16864436 INFO @ Mon, 29 Jun 2020 21:49:17: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:49:18: 12000000 INFO @ Mon, 29 Jun 2020 21:49:18: #1 tags after filtering in treatment: 16864436 INFO @ Mon, 29 Jun 2020 21:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:18: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:18: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:19: #2 number of paired peaks: 181 WARNING @ Mon, 29 Jun 2020 21:49:19: 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 @ Mon, 29 Jun 2020 21:49:19: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:19: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:19: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:19: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:19: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 21:49:19: #2 alternative fragment length(s) may be 1,33,529,598 bps INFO @ Mon, 29 Jun 2020 21:49:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.10_model.r WARNING @ Mon, 29 Jun 2020 21:49:19: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:19: #2 You may need to consider one of the other alternative d(s): 1,33,529,598 WARNING @ Mon, 29 Jun 2020 21:49:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:49:19: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:49:23: 13000000 INFO @ Mon, 29 Jun 2020 21:49:28: 14000000 INFO @ Mon, 29 Jun 2020 21:49:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:49:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:49:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.05_summits.bed INFO @ Mon, 29 Jun 2020 21:49:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3234 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:49:33: 15000000 INFO @ Mon, 29 Jun 2020 21:49:39: 16000000 INFO @ Mon, 29 Jun 2020 21:49:43: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 21:49:43: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 21:49:43: #1 total tags in treatment: 16864436 INFO @ Mon, 29 Jun 2020 21:49:43: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:49:44: #1 tags after filtering in treatment: 16864436 INFO @ Mon, 29 Jun 2020 21:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:44: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:45: #2 number of paired peaks: 181 WARNING @ Mon, 29 Jun 2020 21:49:45: 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 @ Mon, 29 Jun 2020 21:49:45: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:45: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:45: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:45: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:45: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 21:49:45: #2 alternative fragment length(s) may be 1,33,529,598 bps INFO @ Mon, 29 Jun 2020 21:49:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.20_model.r WARNING @ Mon, 29 Jun 2020 21:49:45: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:45: #2 You may need to consider one of the other alternative d(s): 1,33,529,598 WARNING @ Mon, 29 Jun 2020 21:49:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:49:45: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:49:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.10_summits.bed INFO @ Mon, 29 Jun 2020 21:50:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (378 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:50:17: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:50:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:50:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059224/SRX059224.20_summits.bed INFO @ Mon, 29 Jun 2020 21:50:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (73 records, 4 fields): 2 millis CompletedMACS2peakCalling