Job ID = 6366069 SRX = SRX059241 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:27:29 prefetch.2.10.7: 1) Downloading 'SRR190681'... 2020-06-15T22:27:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:28:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:28:32 prefetch.2.10.7: 'SRR190681' is valid 2020-06-15T22:28:32 prefetch.2.10.7: 1) 'SRR190681' was downloaded successfully Read 15415791 spots for SRR190681/SRR190681.sra Written 15415791 spots for SRR190681/SRR190681.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: 00:02:41 15415791 reads; of these: 15415791 (100.00%) were unpaired; of these: 537270 (3.49%) aligned 0 times 12038351 (78.09%) aligned exactly 1 time 2840170 (18.42%) aligned >1 times 96.51% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 1467132 / 14878521 = 0.0986 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 07:35:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.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 07:35:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:40: 1000000 INFO @ Tue, 16 Jun 2020 07:35:45: 2000000 INFO @ Tue, 16 Jun 2020 07:35:50: 3000000 INFO @ Tue, 16 Jun 2020 07:35:56: 4000000 INFO @ Tue, 16 Jun 2020 07:36:01: 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 07:36:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.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 07:36:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:06: 6000000 INFO @ Tue, 16 Jun 2020 07:36:11: 1000000 INFO @ Tue, 16 Jun 2020 07:36:12: 7000000 INFO @ Tue, 16 Jun 2020 07:36:16: 2000000 INFO @ Tue, 16 Jun 2020 07:36:17: 8000000 INFO @ Tue, 16 Jun 2020 07:36:22: 3000000 INFO @ Tue, 16 Jun 2020 07:36:23: 9000000 INFO @ Tue, 16 Jun 2020 07:36:28: 4000000 INFO @ Tue, 16 Jun 2020 07:36:29: 10000000 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 07:36:33: 5000000 INFO @ Tue, 16 Jun 2020 07:36:34: 11000000 INFO @ Tue, 16 Jun 2020 07:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.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 07:36:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:39: 6000000 INFO @ Tue, 16 Jun 2020 07:36:40: 12000000 INFO @ Tue, 16 Jun 2020 07:36:41: 1000000 INFO @ Tue, 16 Jun 2020 07:36:45: 7000000 INFO @ Tue, 16 Jun 2020 07:36:46: 13000000 INFO @ Tue, 16 Jun 2020 07:36:47: 2000000 INFO @ Tue, 16 Jun 2020 07:36:48: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:36:48: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:36:48: #1 total tags in treatment: 13411389 INFO @ Tue, 16 Jun 2020 07:36:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:48: #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 07:36:48: #1 tags after filtering in treatment: 13411389 INFO @ Tue, 16 Jun 2020 07:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:49: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 07:36:49: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 07:36:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:49: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:36:49: #2 alternative fragment length(s) may be 2,34 bps INFO @ Tue, 16 Jun 2020 07:36:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.05_model.r WARNING @ Tue, 16 Jun 2020 07:36:49: #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 07:36:49: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Tue, 16 Jun 2020 07:36:49: #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 07:36:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:51: 8000000 INFO @ Tue, 16 Jun 2020 07:36:52: 3000000 INFO @ Tue, 16 Jun 2020 07:36:56: 9000000 INFO @ Tue, 16 Jun 2020 07:36:58: 4000000 INFO @ Tue, 16 Jun 2020 07:37:01: 10000000 INFO @ Tue, 16 Jun 2020 07:37:03: 5000000 INFO @ Tue, 16 Jun 2020 07:37:07: 11000000 INFO @ Tue, 16 Jun 2020 07:37:09: 6000000 INFO @ Tue, 16 Jun 2020 07:37:12: 12000000 INFO @ Tue, 16 Jun 2020 07:37:14: 7000000 INFO @ Tue, 16 Jun 2020 07:37:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:18: 13000000 INFO @ Tue, 16 Jun 2020 07:37:19: 8000000 INFO @ Tue, 16 Jun 2020 07:37:20: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:37:20: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:37:20: #1 total tags in treatment: 13411389 INFO @ Tue, 16 Jun 2020 07:37:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:20: #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 07:37:20: #1 tags after filtering in treatment: 13411389 INFO @ Tue, 16 Jun 2020 07:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:20: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:21: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 07:37:21: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 07:37:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:21: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:37:21: #2 alternative fragment length(s) may be 2,34 bps INFO @ Tue, 16 Jun 2020 07:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.10_model.r WARNING @ Tue, 16 Jun 2020 07:37:21: #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 07:37:21: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Tue, 16 Jun 2020 07:37:21: #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 07:37:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:25: 9000000 INFO @ Tue, 16 Jun 2020 07:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.05_summits.bed INFO @ Tue, 16 Jun 2020 07:37:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1397 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:37:30: 10000000 INFO @ Tue, 16 Jun 2020 07:37:35: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:37:40: 12000000 INFO @ Tue, 16 Jun 2020 07:37:45: 13000000 INFO @ Tue, 16 Jun 2020 07:37:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:47: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:37:47: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:37:47: #1 total tags in treatment: 13411389 INFO @ Tue, 16 Jun 2020 07:37:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:47: #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 07:37:48: #1 tags after filtering in treatment: 13411389 INFO @ Tue, 16 Jun 2020 07:37:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:49: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 07:37:49: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 07:37:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:49: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:37:49: #2 alternative fragment length(s) may be 2,34 bps INFO @ Tue, 16 Jun 2020 07:37:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.20_model.r WARNING @ Tue, 16 Jun 2020 07:37:49: #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 07:37:49: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Tue, 16 Jun 2020 07:37:49: #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 07:37:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.10_summits.bed INFO @ Tue, 16 Jun 2020 07:37:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (772 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:38:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059241/SRX059241.20_summits.bed INFO @ Tue, 16 Jun 2020 07:38:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling