Job ID = 6366962 SRX = SRX2576661 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:38 prefetch.2.10.7: 1) Downloading 'SRR5272618'... 2020-06-15T23:06:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:30 prefetch.2.10.7: 'SRR5272618' is valid 2020-06-15T23:07:30 prefetch.2.10.7: 1) 'SRR5272618' was downloaded successfully Read 14590761 spots for SRR5272618/SRR5272618.sra Written 14590761 spots for SRR5272618/SRR5272618.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: 00:02:21 14590761 reads; of these: 14590761 (100.00%) were unpaired; of these: 303734 (2.08%) aligned 0 times 11932727 (81.78%) aligned exactly 1 time 2354300 (16.14%) aligned >1 times 97.92% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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_rmdupse_core] 1255280 / 14287027 = 0.0879 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 08:13:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.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 08:13:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:49: 1000000 INFO @ Tue, 16 Jun 2020 08:13:54: 2000000 INFO @ Tue, 16 Jun 2020 08:13:58: 3000000 INFO @ Tue, 16 Jun 2020 08:14:03: 4000000 INFO @ Tue, 16 Jun 2020 08:14:08: 5000000 INFO @ Tue, 16 Jun 2020 08:14:12: 6000000 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 08:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.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 08:14:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:17: 7000000 INFO @ Tue, 16 Jun 2020 08:14:19: 1000000 INFO @ Tue, 16 Jun 2020 08:14:22: 8000000 INFO @ Tue, 16 Jun 2020 08:14:24: 2000000 INFO @ Tue, 16 Jun 2020 08:14:27: 9000000 INFO @ Tue, 16 Jun 2020 08:14:29: 3000000 INFO @ Tue, 16 Jun 2020 08:14:31: 10000000 INFO @ Tue, 16 Jun 2020 08:14:34: 4000000 INFO @ Tue, 16 Jun 2020 08:14:36: 11000000 INFO @ Tue, 16 Jun 2020 08:14:39: 5000000 INFO @ Tue, 16 Jun 2020 08:14:41: 12000000 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 08:14:44: 6000000 INFO @ Tue, 16 Jun 2020 08:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.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 08:14:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:46: 13000000 INFO @ Tue, 16 Jun 2020 08:14:46: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:14:46: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:14:46: #1 total tags in treatment: 13031747 INFO @ Tue, 16 Jun 2020 08:14:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:46: #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 08:14:46: #1 tags after filtering in treatment: 13031747 INFO @ Tue, 16 Jun 2020 08:14:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:47: #2 number of paired peaks: 254 WARNING @ Tue, 16 Jun 2020 08:14:47: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:47: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:14:47: #2 alternative fragment length(s) may be 1,34,522,583 bps INFO @ Tue, 16 Jun 2020 08:14:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.05_model.r WARNING @ Tue, 16 Jun 2020 08:14:47: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:47: #2 You may need to consider one of the other alternative d(s): 1,34,522,583 WARNING @ Tue, 16 Jun 2020 08:14:47: #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 08:14:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:49: 7000000 INFO @ Tue, 16 Jun 2020 08:14:49: 1000000 INFO @ Tue, 16 Jun 2020 08:14:54: 8000000 INFO @ Tue, 16 Jun 2020 08:14:54: 2000000 INFO @ Tue, 16 Jun 2020 08:14:59: 9000000 INFO @ Tue, 16 Jun 2020 08:14:59: 3000000 INFO @ Tue, 16 Jun 2020 08:15:04: 10000000 INFO @ Tue, 16 Jun 2020 08:15:04: 4000000 INFO @ Tue, 16 Jun 2020 08:15:09: 11000000 INFO @ Tue, 16 Jun 2020 08:15:09: 5000000 INFO @ Tue, 16 Jun 2020 08:15:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:14: 12000000 INFO @ Tue, 16 Jun 2020 08:15:14: 6000000 INFO @ Tue, 16 Jun 2020 08:15:19: 13000000 INFO @ Tue, 16 Jun 2020 08:15:19: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:15:19: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:15:19: #1 total tags in treatment: 13031747 INFO @ Tue, 16 Jun 2020 08:15:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:19: #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 08:15:19: #1 tags after filtering in treatment: 13031747 INFO @ Tue, 16 Jun 2020 08:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:19: 7000000 INFO @ Tue, 16 Jun 2020 08:15:20: #2 number of paired peaks: 254 WARNING @ Tue, 16 Jun 2020 08:15:20: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:20: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:15:20: #2 alternative fragment length(s) may be 1,34,522,583 bps INFO @ Tue, 16 Jun 2020 08:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.10_model.r WARNING @ Tue, 16 Jun 2020 08:15:20: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:20: #2 You may need to consider one of the other alternative d(s): 1,34,522,583 WARNING @ Tue, 16 Jun 2020 08:15:20: #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 08:15:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (548 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:24: 8000000 INFO @ Tue, 16 Jun 2020 08:15:29: 9000000 INFO @ Tue, 16 Jun 2020 08:15:34: 10000000 INFO @ Tue, 16 Jun 2020 08:15:39: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:44: 12000000 INFO @ Tue, 16 Jun 2020 08:15:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:48: 13000000 INFO @ Tue, 16 Jun 2020 08:15:49: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:15:49: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:15:49: #1 total tags in treatment: 13031747 INFO @ Tue, 16 Jun 2020 08:15:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:49: #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 08:15:49: #1 tags after filtering in treatment: 13031747 INFO @ Tue, 16 Jun 2020 08:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:50: #2 number of paired peaks: 254 WARNING @ Tue, 16 Jun 2020 08:15:50: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:50: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:15:50: #2 alternative fragment length(s) may be 1,34,522,583 bps INFO @ Tue, 16 Jun 2020 08:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.20_model.r WARNING @ Tue, 16 Jun 2020 08:15:50: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:50: #2 You may need to consider one of the other alternative d(s): 1,34,522,583 WARNING @ Tue, 16 Jun 2020 08:15:50: #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 08:15:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576661/SRX2576661.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 0 millis CompletedMACS2peakCalling