Job ID = 6368676 SRX = SRX5402703 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:12 prefetch.2.10.7: 1) Downloading 'SRR8602937'... 2020-06-16T00:30:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:08 prefetch.2.10.7: 'SRR8602937' is valid 2020-06-16T00:32:08 prefetch.2.10.7: 1) 'SRR8602937' was downloaded successfully 2020-06-16T00:32:08 prefetch.2.10.7: 'SRR8602937' has 0 unresolved dependencies Read 20392638 spots for SRR8602937/SRR8602937.sra Written 20392638 spots for SRR8602937/SRR8602937.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: 00:04:45 20392638 reads; of these: 20392638 (100.00%) were unpaired; of these: 218820 (1.07%) aligned 0 times 15398361 (75.51%) aligned exactly 1 time 4775457 (23.42%) aligned >1 times 98.93% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 7268063 / 20173818 = 0.3603 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 09:41:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.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 09:41:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:53: 1000000 INFO @ Tue, 16 Jun 2020 09:41:58: 2000000 INFO @ Tue, 16 Jun 2020 09:42:05: 3000000 INFO @ Tue, 16 Jun 2020 09:42:11: 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 09:42:17: 5000000 INFO @ Tue, 16 Jun 2020 09:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.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 09:42:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:23: 1000000 INFO @ Tue, 16 Jun 2020 09:42:24: 6000000 INFO @ Tue, 16 Jun 2020 09:42:29: 2000000 INFO @ Tue, 16 Jun 2020 09:42:30: 7000000 INFO @ Tue, 16 Jun 2020 09:42:35: 3000000 INFO @ Tue, 16 Jun 2020 09:42:36: 8000000 INFO @ Tue, 16 Jun 2020 09:42:41: 4000000 INFO @ Tue, 16 Jun 2020 09:42:43: 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 09:42:47: 5000000 INFO @ Tue, 16 Jun 2020 09:42:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.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 09:42:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:49: 10000000 INFO @ Tue, 16 Jun 2020 09:42:53: 6000000 INFO @ Tue, 16 Jun 2020 09:42:56: 1000000 INFO @ Tue, 16 Jun 2020 09:42:56: 11000000 INFO @ Tue, 16 Jun 2020 09:42:59: 7000000 INFO @ Tue, 16 Jun 2020 09:43:04: 2000000 INFO @ Tue, 16 Jun 2020 09:43:04: 12000000 INFO @ Tue, 16 Jun 2020 09:43:05: 8000000 INFO @ Tue, 16 Jun 2020 09:43:10: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:43:10: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:43:10: #1 total tags in treatment: 12905755 INFO @ Tue, 16 Jun 2020 09:43:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:10: #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 09:43:10: #1 tags after filtering in treatment: 12905755 INFO @ Tue, 16 Jun 2020 09:43:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:10: 3000000 INFO @ Tue, 16 Jun 2020 09:43:11: #2 number of paired peaks: 608 WARNING @ Tue, 16 Jun 2020 09:43:11: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:11: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:43:11: #2 alternative fragment length(s) may be 2,54,570 bps INFO @ Tue, 16 Jun 2020 09:43:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.05_model.r WARNING @ Tue, 16 Jun 2020 09:43:11: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:11: #2 You may need to consider one of the other alternative d(s): 2,54,570 WARNING @ Tue, 16 Jun 2020 09:43:11: #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 09:43:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:12: 9000000 INFO @ Tue, 16 Jun 2020 09:43:17: 4000000 INFO @ Tue, 16 Jun 2020 09:43:18: 10000000 INFO @ Tue, 16 Jun 2020 09:43:23: 5000000 INFO @ Tue, 16 Jun 2020 09:43:24: 11000000 INFO @ Tue, 16 Jun 2020 09:43:30: 6000000 INFO @ Tue, 16 Jun 2020 09:43:30: 12000000 INFO @ Tue, 16 Jun 2020 09:43:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:43:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:43:35: #1 total tags in treatment: 12905755 INFO @ Tue, 16 Jun 2020 09:43:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:35: #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 09:43:36: #1 tags after filtering in treatment: 12905755 INFO @ Tue, 16 Jun 2020 09:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:36: 7000000 INFO @ Tue, 16 Jun 2020 09:43:37: #2 number of paired peaks: 608 WARNING @ Tue, 16 Jun 2020 09:43:37: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:37: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:43:37: #2 alternative fragment length(s) may be 2,54,570 bps INFO @ Tue, 16 Jun 2020 09:43:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:37: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:37: #2 You may need to consider one of the other alternative d(s): 2,54,570 WARNING @ Tue, 16 Jun 2020 09:43:37: #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 09:43:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:43: 8000000 INFO @ Tue, 16 Jun 2020 09:43:49: 9000000 INFO @ Tue, 16 Jun 2020 09:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.05_summits.bed INFO @ Tue, 16 Jun 2020 09:43:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2341 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:55: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:44:01: 11000000 INFO @ Tue, 16 Jun 2020 09:44:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:07: 12000000 INFO @ Tue, 16 Jun 2020 09:44:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:44:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:44:13: #1 total tags in treatment: 12905755 INFO @ Tue, 16 Jun 2020 09:44:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:13: #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 09:44:13: #1 tags after filtering in treatment: 12905755 INFO @ Tue, 16 Jun 2020 09:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:14: #2 number of paired peaks: 608 WARNING @ Tue, 16 Jun 2020 09:44:14: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:14: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:44:14: #2 alternative fragment length(s) may be 2,54,570 bps INFO @ Tue, 16 Jun 2020 09:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.20_model.r WARNING @ Tue, 16 Jun 2020 09:44:14: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:14: #2 You may need to consider one of the other alternative d(s): 2,54,570 WARNING @ Tue, 16 Jun 2020 09:44:14: #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 09:44:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.10_summits.bed INFO @ Tue, 16 Jun 2020 09:44:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (841 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:44:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402703/SRX5402703.20_summits.bed INFO @ Tue, 16 Jun 2020 09:44:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling