Job ID = 6368747 SRX = SRX5402770 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:04 prefetch.2.10.7: 1) Downloading 'SRR8603004'... 2020-06-16T00:27:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:39 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:39 prefetch.2.10.7: 1) 'SRR8603004' was downloaded successfully Read 18322369 spots for SRR8603004/SRR8603004.sra Written 18322369 spots for SRR8603004/SRR8603004.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: 00:04:05 18322369 reads; of these: 18322369 (100.00%) were unpaired; of these: 1465440 (8.00%) aligned 0 times 14037533 (76.61%) aligned exactly 1 time 2819396 (15.39%) aligned >1 times 92.00% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 6039665 / 16856929 = 0.3583 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 09:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.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 09:41:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:56: 1000000 INFO @ Tue, 16 Jun 2020 09:42:02: 2000000 INFO @ Tue, 16 Jun 2020 09:42:08: 3000000 INFO @ Tue, 16 Jun 2020 09:42:14: 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 09:42:20: 5000000 INFO @ Tue, 16 Jun 2020 09:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.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 09:42:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:26: 6000000 INFO @ Tue, 16 Jun 2020 09:42:27: 1000000 INFO @ Tue, 16 Jun 2020 09:42:33: 7000000 INFO @ Tue, 16 Jun 2020 09:42:33: 2000000 INFO @ Tue, 16 Jun 2020 09:42:39: 8000000 INFO @ Tue, 16 Jun 2020 09:42:40: 3000000 INFO @ Tue, 16 Jun 2020 09:42:46: 9000000 INFO @ Tue, 16 Jun 2020 09:42:47: 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 09:42:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.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 09:42:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:53: 10000000 INFO @ Tue, 16 Jun 2020 09:42:53: 5000000 INFO @ Tue, 16 Jun 2020 09:42:57: 1000000 INFO @ Tue, 16 Jun 2020 09:42:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:58: #1 total tags in treatment: 10817264 INFO @ Tue, 16 Jun 2020 09:42:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:58: #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 09:42:58: #1 tags after filtering in treatment: 10817264 INFO @ Tue, 16 Jun 2020 09:42:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:59: #2 number of paired peaks: 423 WARNING @ Tue, 16 Jun 2020 09:42:59: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:59: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:42:59: #2 alternative fragment length(s) may be 2,44,571 bps INFO @ Tue, 16 Jun 2020 09:42:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.05_model.r WARNING @ Tue, 16 Jun 2020 09:42:59: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:59: #2 You may need to consider one of the other alternative d(s): 2,44,571 WARNING @ Tue, 16 Jun 2020 09:42:59: #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 09:42:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:00: 6000000 INFO @ Tue, 16 Jun 2020 09:43:04: 2000000 INFO @ Tue, 16 Jun 2020 09:43:07: 7000000 INFO @ Tue, 16 Jun 2020 09:43:11: 3000000 INFO @ Tue, 16 Jun 2020 09:43:14: 8000000 INFO @ Tue, 16 Jun 2020 09:43:17: 4000000 INFO @ Tue, 16 Jun 2020 09:43:20: 9000000 INFO @ Tue, 16 Jun 2020 09:43:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:24: 5000000 INFO @ Tue, 16 Jun 2020 09:43:27: 10000000 INFO @ Tue, 16 Jun 2020 09:43:30: 6000000 INFO @ Tue, 16 Jun 2020 09:43:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:43:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:43:32: #1 total tags in treatment: 10817264 INFO @ Tue, 16 Jun 2020 09:43:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:32: #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 09:43:33: #1 tags after filtering in treatment: 10817264 INFO @ Tue, 16 Jun 2020 09:43:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.05_summits.bed INFO @ Tue, 16 Jun 2020 09:43:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (724 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:33: #2 number of paired peaks: 423 WARNING @ Tue, 16 Jun 2020 09:43:33: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:34: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:43:34: #2 alternative fragment length(s) may be 2,44,571 bps INFO @ Tue, 16 Jun 2020 09:43:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:34: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:34: #2 You may need to consider one of the other alternative d(s): 2,44,571 WARNING @ Tue, 16 Jun 2020 09:43:34: #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 09:43:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:37: 7000000 INFO @ Tue, 16 Jun 2020 09:43:43: 8000000 INFO @ Tue, 16 Jun 2020 09:43:49: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:55: 10000000 INFO @ Tue, 16 Jun 2020 09:43:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:44:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:44:00: #1 total tags in treatment: 10817264 INFO @ Tue, 16 Jun 2020 09:44:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:00: #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 09:44:00: #1 tags after filtering in treatment: 10817264 INFO @ Tue, 16 Jun 2020 09:44:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:01: #2 number of paired peaks: 423 WARNING @ Tue, 16 Jun 2020 09:44:01: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:01: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:44:01: #2 alternative fragment length(s) may be 2,44,571 bps INFO @ Tue, 16 Jun 2020 09:44:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.20_model.r WARNING @ Tue, 16 Jun 2020 09:44:01: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:01: #2 You may need to consider one of the other alternative d(s): 2,44,571 WARNING @ Tue, 16 Jun 2020 09:44:01: #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 09:44:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.10_summits.bed INFO @ Tue, 16 Jun 2020 09:44:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (473 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:44:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402770/SRX5402770.20_summits.bed INFO @ Tue, 16 Jun 2020 09:44:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling