Job ID = 6366056 SRX = SRX059228 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:52 prefetch.2.10.7: 1) Downloading 'SRR190668'... 2020-06-15T22:46:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:48:52 prefetch.2.10.7: 1) 'SRR190668' was downloaded successfully Read 19141045 spots for SRR190668/SRR190668.sra Written 19141045 spots for SRR190668/SRR190668.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: 00:03:47 19141045 reads; of these: 19141045 (100.00%) were unpaired; of these: 247041 (1.29%) aligned 0 times 15164801 (79.23%) aligned exactly 1 time 3729203 (19.48%) aligned >1 times 98.71% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 2762749 / 18894004 = 0.1462 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 07:58:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.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 07:58:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:50: 1000000 INFO @ Tue, 16 Jun 2020 07:58:56: 2000000 INFO @ Tue, 16 Jun 2020 07:59:02: 3000000 INFO @ Tue, 16 Jun 2020 07:59:08: 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 07:59:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.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 07:59:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:14: 5000000 INFO @ Tue, 16 Jun 2020 07:59:21: 1000000 INFO @ Tue, 16 Jun 2020 07:59:21: 6000000 INFO @ Tue, 16 Jun 2020 07:59:27: 2000000 INFO @ Tue, 16 Jun 2020 07:59:27: 7000000 INFO @ Tue, 16 Jun 2020 07:59:33: 3000000 INFO @ Tue, 16 Jun 2020 07:59:33: 8000000 INFO @ Tue, 16 Jun 2020 07:59:40: 4000000 INFO @ Tue, 16 Jun 2020 07:59:40: 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 07:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.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 07:59:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:46: 5000000 INFO @ Tue, 16 Jun 2020 07:59:46: 10000000 INFO @ Tue, 16 Jun 2020 07:59:51: 1000000 INFO @ Tue, 16 Jun 2020 07:59:52: 6000000 INFO @ Tue, 16 Jun 2020 07:59:53: 11000000 INFO @ Tue, 16 Jun 2020 07:59:57: 2000000 INFO @ Tue, 16 Jun 2020 07:59:59: 7000000 INFO @ Tue, 16 Jun 2020 08:00:00: 12000000 INFO @ Tue, 16 Jun 2020 08:00:04: 3000000 INFO @ Tue, 16 Jun 2020 08:00:05: 8000000 INFO @ Tue, 16 Jun 2020 08:00:07: 13000000 INFO @ Tue, 16 Jun 2020 08:00:11: 4000000 INFO @ Tue, 16 Jun 2020 08:00:12: 9000000 INFO @ Tue, 16 Jun 2020 08:00:14: 14000000 INFO @ Tue, 16 Jun 2020 08:00:18: 5000000 INFO @ Tue, 16 Jun 2020 08:00:18: 10000000 INFO @ Tue, 16 Jun 2020 08:00:20: 15000000 INFO @ Tue, 16 Jun 2020 08:00:24: 6000000 INFO @ Tue, 16 Jun 2020 08:00:25: 11000000 INFO @ Tue, 16 Jun 2020 08:00:27: 16000000 INFO @ Tue, 16 Jun 2020 08:00:28: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:00:28: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:00:28: #1 total tags in treatment: 16131255 INFO @ Tue, 16 Jun 2020 08:00:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:28: #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 08:00:28: #1 tags after filtering in treatment: 16131255 INFO @ Tue, 16 Jun 2020 08:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:30: #2 number of paired peaks: 261 WARNING @ Tue, 16 Jun 2020 08:00:30: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:30: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:00:30: #2 alternative fragment length(s) may be 2,31 bps INFO @ Tue, 16 Jun 2020 08:00:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.05_model.r WARNING @ Tue, 16 Jun 2020 08:00:30: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:00:30: #2 You may need to consider one of the other alternative d(s): 2,31 WARNING @ Tue, 16 Jun 2020 08:00:30: #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 08:00:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:31: 7000000 INFO @ Tue, 16 Jun 2020 08:00:32: 12000000 INFO @ Tue, 16 Jun 2020 08:00:37: 8000000 INFO @ Tue, 16 Jun 2020 08:00:38: 13000000 INFO @ Tue, 16 Jun 2020 08:00:44: 9000000 INFO @ Tue, 16 Jun 2020 08:00:45: 14000000 INFO @ Tue, 16 Jun 2020 08:00:50: 10000000 INFO @ Tue, 16 Jun 2020 08:00:51: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:00:57: 11000000 INFO @ Tue, 16 Jun 2020 08:00:57: 16000000 INFO @ Tue, 16 Jun 2020 08:00:58: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:00:58: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:00:58: #1 total tags in treatment: 16131255 INFO @ Tue, 16 Jun 2020 08:00:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:58: #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 08:00:59: #1 tags after filtering in treatment: 16131255 INFO @ Tue, 16 Jun 2020 08:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:00: #2 number of paired peaks: 261 WARNING @ Tue, 16 Jun 2020 08:01:00: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:00: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:01:00: #2 alternative fragment length(s) may be 2,31 bps INFO @ Tue, 16 Jun 2020 08:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.10_model.r WARNING @ Tue, 16 Jun 2020 08:01:00: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:01:00: #2 You may need to consider one of the other alternative d(s): 2,31 WARNING @ Tue, 16 Jun 2020 08:01:00: #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 08:01:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:04: 12000000 INFO @ Tue, 16 Jun 2020 08:01:10: 13000000 INFO @ Tue, 16 Jun 2020 08:01:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.05_summits.bed INFO @ Tue, 16 Jun 2020 08:01:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7609 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:17: 14000000 INFO @ Tue, 16 Jun 2020 08:01:23: 15000000 INFO @ Tue, 16 Jun 2020 08:01:29: 16000000 INFO @ Tue, 16 Jun 2020 08:01:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:30: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:01:30: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:01:30: #1 total tags in treatment: 16131255 INFO @ Tue, 16 Jun 2020 08:01:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:30: #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 08:01:30: #1 tags after filtering in treatment: 16131255 INFO @ Tue, 16 Jun 2020 08:01:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:31: #2 number of paired peaks: 261 WARNING @ Tue, 16 Jun 2020 08:01:31: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:32: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:01:32: #2 alternative fragment length(s) may be 2,31 bps INFO @ Tue, 16 Jun 2020 08:01:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.20_model.r WARNING @ Tue, 16 Jun 2020 08:01:32: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:01:32: #2 You may need to consider one of the other alternative d(s): 2,31 WARNING @ Tue, 16 Jun 2020 08:01:32: #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 08:01:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.10_summits.bed INFO @ Tue, 16 Jun 2020 08:01:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (998 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059228/SRX059228.20_summits.bed INFO @ Tue, 16 Jun 2020 08:02:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 1 millis CompletedMACS2peakCalling