Job ID = 6368716 SRX = SRX5402740 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:05 prefetch.2.10.7: 1) Downloading 'SRR8602974'... 2020-06-16T00:26:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:39 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:39 prefetch.2.10.7: 1) 'SRR8602974' was downloaded successfully Read 29950235 spots for SRR8602974/SRR8602974.sra Written 29950235 spots for SRR8602974/SRR8602974.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: 00:07:59 29950235 reads; of these: 29950235 (100.00%) were unpaired; of these: 2470596 (8.25%) aligned 0 times 15503282 (51.76%) aligned exactly 1 time 11976357 (39.99%) aligned >1 times 91.75% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 13245782 / 27479639 = 0.4820 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 09:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.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 09:43:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:50: 1000000 INFO @ Tue, 16 Jun 2020 09:43:56: 2000000 INFO @ Tue, 16 Jun 2020 09:44:01: 3000000 INFO @ Tue, 16 Jun 2020 09:44:06: 4000000 INFO @ Tue, 16 Jun 2020 09:44:11: 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 @ Tue, 16 Jun 2020 09:44:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.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 09:44:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:16: 6000000 INFO @ Tue, 16 Jun 2020 09:44:21: 1000000 INFO @ Tue, 16 Jun 2020 09:44:21: 7000000 INFO @ Tue, 16 Jun 2020 09:44:25: 2000000 INFO @ Tue, 16 Jun 2020 09:44:26: 8000000 INFO @ Tue, 16 Jun 2020 09:44:31: 3000000 INFO @ Tue, 16 Jun 2020 09:44:31: 9000000 INFO @ Tue, 16 Jun 2020 09:44:36: 4000000 INFO @ Tue, 16 Jun 2020 09:44:36: 10000000 INFO @ Tue, 16 Jun 2020 09:44:41: 5000000 INFO @ Tue, 16 Jun 2020 09:44:41: 11000000 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 09:44:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.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 09:44:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:46: 6000000 INFO @ Tue, 16 Jun 2020 09:44:46: 12000000 INFO @ Tue, 16 Jun 2020 09:44:50: 7000000 INFO @ Tue, 16 Jun 2020 09:44:50: 1000000 INFO @ Tue, 16 Jun 2020 09:44:51: 13000000 INFO @ Tue, 16 Jun 2020 09:44:55: 8000000 INFO @ Tue, 16 Jun 2020 09:44:55: 2000000 INFO @ Tue, 16 Jun 2020 09:44:56: 14000000 INFO @ Tue, 16 Jun 2020 09:44:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:44:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:44:57: #1 total tags in treatment: 14233857 INFO @ Tue, 16 Jun 2020 09:44:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:57: #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 09:44:57: #1 tags after filtering in treatment: 14233857 INFO @ Tue, 16 Jun 2020 09:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:58: #2 number of paired peaks: 3041 INFO @ Tue, 16 Jun 2020 09:44:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:59: #2 predicted fragment length is 97 bps INFO @ Tue, 16 Jun 2020 09:44:59: #2 alternative fragment length(s) may be 4,97 bps INFO @ Tue, 16 Jun 2020 09:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.05_model.r WARNING @ Tue, 16 Jun 2020 09:44:59: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:59: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Tue, 16 Jun 2020 09:44:59: #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 09:44:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:00: 9000000 INFO @ Tue, 16 Jun 2020 09:45:00: 3000000 INFO @ Tue, 16 Jun 2020 09:45:05: 10000000 INFO @ Tue, 16 Jun 2020 09:45:05: 4000000 INFO @ Tue, 16 Jun 2020 09:45:10: 11000000 INFO @ Tue, 16 Jun 2020 09:45:10: 5000000 INFO @ Tue, 16 Jun 2020 09:45:15: 12000000 INFO @ Tue, 16 Jun 2020 09:45:15: 6000000 INFO @ Tue, 16 Jun 2020 09:45:20: 13000000 INFO @ Tue, 16 Jun 2020 09:45:20: 7000000 INFO @ Tue, 16 Jun 2020 09:45:25: 14000000 INFO @ Tue, 16 Jun 2020 09:45:25: 8000000 INFO @ Tue, 16 Jun 2020 09:45:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:26: #1 total tags in treatment: 14233857 INFO @ Tue, 16 Jun 2020 09:45:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:26: #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 09:45:26: #1 tags after filtering in treatment: 14233857 INFO @ Tue, 16 Jun 2020 09:45:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:27: #2 number of paired peaks: 3041 INFO @ Tue, 16 Jun 2020 09:45:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:28: #2 predicted fragment length is 97 bps INFO @ Tue, 16 Jun 2020 09:45:28: #2 alternative fragment length(s) may be 4,97 bps INFO @ Tue, 16 Jun 2020 09:45:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.10_model.r WARNING @ Tue, 16 Jun 2020 09:45:28: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:28: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Tue, 16 Jun 2020 09:45:28: #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 09:45:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:30: 9000000 INFO @ Tue, 16 Jun 2020 09:45:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:35: 10000000 INFO @ Tue, 16 Jun 2020 09:45:39: 11000000 INFO @ Tue, 16 Jun 2020 09:45:44: 12000000 INFO @ Tue, 16 Jun 2020 09:45:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.05_summits.bed INFO @ Tue, 16 Jun 2020 09:45:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8956 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:49: 13000000 INFO @ Tue, 16 Jun 2020 09:45:54: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:55: #1 total tags in treatment: 14233857 INFO @ Tue, 16 Jun 2020 09:45:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:55: #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 09:45:56: #1 tags after filtering in treatment: 14233857 INFO @ Tue, 16 Jun 2020 09:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:57: #2 number of paired peaks: 3041 INFO @ Tue, 16 Jun 2020 09:45:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:57: #2 predicted fragment length is 97 bps INFO @ Tue, 16 Jun 2020 09:45:57: #2 alternative fragment length(s) may be 4,97 bps INFO @ Tue, 16 Jun 2020 09:45:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.20_model.r WARNING @ Tue, 16 Jun 2020 09:45:57: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:57: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Tue, 16 Jun 2020 09:45:57: #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 09:45:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.10_summits.bed INFO @ Tue, 16 Jun 2020 09:46:16: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6005 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:46:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402740/SRX5402740.20_summits.bed INFO @ Tue, 16 Jun 2020 09:46:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2821 records, 4 fields): 4 millis CompletedMACS2peakCalling