Job ID = 6368825 SRX = SRX5985678 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:34:29 prefetch.2.10.7: 1) Downloading 'SRR9214983'... 2020-06-16T00:34:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:37:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:37:52 prefetch.2.10.7: 1) 'SRR9214983' was downloaded successfully Read 32897127 spots for SRR9214983/SRR9214983.sra Written 32897127 spots for SRR9214983/SRR9214983.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: 00:10:08 32897127 reads; of these: 32897127 (100.00%) were unpaired; of these: 233302 (0.71%) aligned 0 times 29498711 (89.67%) aligned exactly 1 time 3165114 (9.62%) aligned >1 times 99.29% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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] 7428381 / 32663825 = 0.2274 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 09:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.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 09:57:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:03: 1000000 INFO @ Tue, 16 Jun 2020 09:58:09: 2000000 INFO @ Tue, 16 Jun 2020 09:58:15: 3000000 INFO @ Tue, 16 Jun 2020 09:58:21: 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 09:58:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.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 09:58:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:27: 5000000 INFO @ Tue, 16 Jun 2020 09:58:33: 1000000 INFO @ Tue, 16 Jun 2020 09:58:33: 6000000 INFO @ Tue, 16 Jun 2020 09:58:39: 2000000 INFO @ Tue, 16 Jun 2020 09:58:40: 7000000 INFO @ Tue, 16 Jun 2020 09:58:44: 3000000 INFO @ Tue, 16 Jun 2020 09:58:46: 8000000 INFO @ Tue, 16 Jun 2020 09:58:50: 4000000 INFO @ Tue, 16 Jun 2020 09:58:52: 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 09:58:56: 5000000 INFO @ Tue, 16 Jun 2020 09:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.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 09:58:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:58: 10000000 INFO @ Tue, 16 Jun 2020 09:59:01: 6000000 INFO @ Tue, 16 Jun 2020 09:59:04: 1000000 INFO @ Tue, 16 Jun 2020 09:59:05: 11000000 INFO @ Tue, 16 Jun 2020 09:59:07: 7000000 INFO @ Tue, 16 Jun 2020 09:59:10: 2000000 INFO @ Tue, 16 Jun 2020 09:59:11: 12000000 INFO @ Tue, 16 Jun 2020 09:59:13: 8000000 INFO @ Tue, 16 Jun 2020 09:59:16: 3000000 INFO @ Tue, 16 Jun 2020 09:59:18: 13000000 INFO @ Tue, 16 Jun 2020 09:59:18: 9000000 INFO @ Tue, 16 Jun 2020 09:59:23: 4000000 INFO @ Tue, 16 Jun 2020 09:59:24: 10000000 INFO @ Tue, 16 Jun 2020 09:59:24: 14000000 INFO @ Tue, 16 Jun 2020 09:59:29: 5000000 INFO @ Tue, 16 Jun 2020 09:59:30: 11000000 INFO @ Tue, 16 Jun 2020 09:59:31: 15000000 INFO @ Tue, 16 Jun 2020 09:59:35: 12000000 INFO @ Tue, 16 Jun 2020 09:59:36: 6000000 INFO @ Tue, 16 Jun 2020 09:59:37: 16000000 INFO @ Tue, 16 Jun 2020 09:59:41: 13000000 INFO @ Tue, 16 Jun 2020 09:59:42: 7000000 INFO @ Tue, 16 Jun 2020 09:59:44: 17000000 INFO @ Tue, 16 Jun 2020 09:59:47: 14000000 INFO @ Tue, 16 Jun 2020 09:59:49: 8000000 INFO @ Tue, 16 Jun 2020 09:59:50: 18000000 INFO @ Tue, 16 Jun 2020 09:59:53: 15000000 INFO @ Tue, 16 Jun 2020 09:59:55: 9000000 INFO @ Tue, 16 Jun 2020 09:59:57: 19000000 INFO @ Tue, 16 Jun 2020 09:59:59: 16000000 INFO @ Tue, 16 Jun 2020 10:00:02: 10000000 INFO @ Tue, 16 Jun 2020 10:00:03: 20000000 INFO @ Tue, 16 Jun 2020 10:00:05: 17000000 INFO @ Tue, 16 Jun 2020 10:00:08: 11000000 INFO @ Tue, 16 Jun 2020 10:00:09: 21000000 INFO @ Tue, 16 Jun 2020 10:00:10: 18000000 INFO @ Tue, 16 Jun 2020 10:00:15: 12000000 INFO @ Tue, 16 Jun 2020 10:00:16: 22000000 INFO @ Tue, 16 Jun 2020 10:00:17: 19000000 INFO @ Tue, 16 Jun 2020 10:00:21: 13000000 INFO @ Tue, 16 Jun 2020 10:00:22: 23000000 INFO @ Tue, 16 Jun 2020 10:00:22: 20000000 INFO @ Tue, 16 Jun 2020 10:00:28: 14000000 INFO @ Tue, 16 Jun 2020 10:00:28: 21000000 INFO @ Tue, 16 Jun 2020 10:00:29: 24000000 INFO @ Tue, 16 Jun 2020 10:00:34: 22000000 INFO @ Tue, 16 Jun 2020 10:00:34: 15000000 INFO @ Tue, 16 Jun 2020 10:00:35: 25000000 INFO @ Tue, 16 Jun 2020 10:00:37: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:00:37: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:00:37: #1 total tags in treatment: 25235444 INFO @ Tue, 16 Jun 2020 10:00:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:00:37: #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 10:00:37: #1 tags after filtering in treatment: 25235444 INFO @ Tue, 16 Jun 2020 10:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:00:37: #1 finished! INFO @ Tue, 16 Jun 2020 10:00:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:00:39: #2 number of paired peaks: 124 WARNING @ Tue, 16 Jun 2020 10:00:39: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 16 Jun 2020 10:00:39: start model_add_line... INFO @ Tue, 16 Jun 2020 10:00:39: start X-correlation... INFO @ Tue, 16 Jun 2020 10:00:39: end of X-cor INFO @ Tue, 16 Jun 2020 10:00:39: #2 finished! INFO @ Tue, 16 Jun 2020 10:00:39: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 10:00:39: #2 alternative fragment length(s) may be 2,38,73,87,119,141,158,197,264,279,301,333,360 bps INFO @ Tue, 16 Jun 2020 10:00:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.05_model.r WARNING @ Tue, 16 Jun 2020 10:00:39: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:00:39: #2 You may need to consider one of the other alternative d(s): 2,38,73,87,119,141,158,197,264,279,301,333,360 WARNING @ Tue, 16 Jun 2020 10:00:39: #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 10:00:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:00:40: 23000000 INFO @ Tue, 16 Jun 2020 10:00:41: 16000000 INFO @ Tue, 16 Jun 2020 10:00:46: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:00:47: 17000000 INFO @ Tue, 16 Jun 2020 10:00:51: 25000000 INFO @ Tue, 16 Jun 2020 10:00:53: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:00:53: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:00:53: #1 total tags in treatment: 25235444 INFO @ Tue, 16 Jun 2020 10:00:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:00:53: #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 10:00:53: #1 tags after filtering in treatment: 25235444 INFO @ Tue, 16 Jun 2020 10:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:00:53: #1 finished! INFO @ Tue, 16 Jun 2020 10:00:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:00:54: 18000000 INFO @ Tue, 16 Jun 2020 10:00:55: #2 number of paired peaks: 124 WARNING @ Tue, 16 Jun 2020 10:00:55: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 16 Jun 2020 10:00:55: start model_add_line... INFO @ Tue, 16 Jun 2020 10:00:55: start X-correlation... INFO @ Tue, 16 Jun 2020 10:00:55: end of X-cor INFO @ Tue, 16 Jun 2020 10:00:55: #2 finished! INFO @ Tue, 16 Jun 2020 10:00:55: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 10:00:55: #2 alternative fragment length(s) may be 2,38,73,87,119,141,158,197,264,279,301,333,360 bps INFO @ Tue, 16 Jun 2020 10:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.10_model.r WARNING @ Tue, 16 Jun 2020 10:00:55: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:00:55: #2 You may need to consider one of the other alternative d(s): 2,38,73,87,119,141,158,197,264,279,301,333,360 WARNING @ Tue, 16 Jun 2020 10:00:55: #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 10:00:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:00: 19000000 INFO @ Tue, 16 Jun 2020 10:01:07: 20000000 INFO @ Tue, 16 Jun 2020 10:01:13: 21000000 INFO @ Tue, 16 Jun 2020 10:01:20: 22000000 INFO @ Tue, 16 Jun 2020 10:01:27: 23000000 INFO @ Tue, 16 Jun 2020 10:01:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:01:33: 24000000 INFO @ Tue, 16 Jun 2020 10:01:40: 25000000 INFO @ Tue, 16 Jun 2020 10:01:42: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:01:42: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:01:42: #1 total tags in treatment: 25235444 INFO @ Tue, 16 Jun 2020 10:01:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:42: #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 10:01:42: #1 tags after filtering in treatment: 25235444 INFO @ Tue, 16 Jun 2020 10:01:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:42: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:44: #2 number of paired peaks: 124 WARNING @ Tue, 16 Jun 2020 10:01:44: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:44: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:44: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:44: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:44: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:44: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 10:01:44: #2 alternative fragment length(s) may be 2,38,73,87,119,141,158,197,264,279,301,333,360 bps INFO @ Tue, 16 Jun 2020 10:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.20_model.r WARNING @ Tue, 16 Jun 2020 10:01:44: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:01:44: #2 You may need to consider one of the other alternative d(s): 2,38,73,87,119,141,158,197,264,279,301,333,360 WARNING @ Tue, 16 Jun 2020 10:01:44: #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 10:01:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.05_summits.bed INFO @ Tue, 16 Jun 2020 10:01:53: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9762 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.10_summits.bed INFO @ Tue, 16 Jun 2020 10:02:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5302 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985678/SRX5985678.20_summits.bed INFO @ Tue, 16 Jun 2020 10:03:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1512 records, 4 fields): 3 millis CompletedMACS2peakCalling