Job ID = 6507927 SRX = SRX495022 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:37:48 prefetch.2.10.7: 1) Downloading 'SRR1198554'... 2020-06-26T13:37:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:39:25 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:39:25 prefetch.2.10.7: 'SRR1198554' is valid 2020-06-26T13:39:25 prefetch.2.10.7: 1) 'SRR1198554' was downloaded successfully Read 13338445 spots for SRR1198554/SRR1198554.sra Written 13338445 spots for SRR1198554/SRR1198554.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: 00:02:47 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88321 (0.66%) aligned 0 times 10992905 (82.42%) aligned exactly 1 time 2257219 (16.92%) aligned >1 times 99.34% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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_rmdupse_core] 2113947 / 13250124 = 0.1595 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 @ Fri, 26 Jun 2020 22:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.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 @ Fri, 26 Jun 2020 22:46:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:46:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:46:36: 1000000 INFO @ Fri, 26 Jun 2020 22:46:42: 2000000 INFO @ Fri, 26 Jun 2020 22:46:49: 3000000 INFO @ Fri, 26 Jun 2020 22:46:55: 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 @ Fri, 26 Jun 2020 22:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.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 @ Fri, 26 Jun 2020 22:46:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:46:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:47:01: 5000000 INFO @ Fri, 26 Jun 2020 22:47:06: 1000000 INFO @ Fri, 26 Jun 2020 22:47:08: 6000000 INFO @ Fri, 26 Jun 2020 22:47:13: 2000000 INFO @ Fri, 26 Jun 2020 22:47:15: 7000000 INFO @ Fri, 26 Jun 2020 22:47:20: 3000000 INFO @ Fri, 26 Jun 2020 22:47:22: 8000000 INFO @ Fri, 26 Jun 2020 22:47:27: 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 @ Fri, 26 Jun 2020 22:47:29: 9000000 INFO @ Fri, 26 Jun 2020 22:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.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 @ Fri, 26 Jun 2020 22:47:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:47:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:47:34: 5000000 INFO @ Fri, 26 Jun 2020 22:47:36: 10000000 INFO @ Fri, 26 Jun 2020 22:47:36: 1000000 INFO @ Fri, 26 Jun 2020 22:47:41: 6000000 INFO @ Fri, 26 Jun 2020 22:47:43: 11000000 INFO @ Fri, 26 Jun 2020 22:47:43: 2000000 INFO @ Fri, 26 Jun 2020 22:47:44: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:47:44: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:47:44: #1 total tags in treatment: 11136177 INFO @ Fri, 26 Jun 2020 22:47:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:47:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:47:44: #1 tags after filtering in treatment: 11136177 INFO @ Fri, 26 Jun 2020 22:47:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:47:44: #1 finished! INFO @ Fri, 26 Jun 2020 22:47:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:47:45: #2 number of paired peaks: 379 WARNING @ Fri, 26 Jun 2020 22:47:45: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Fri, 26 Jun 2020 22:47:45: start model_add_line... INFO @ Fri, 26 Jun 2020 22:47:45: start X-correlation... INFO @ Fri, 26 Jun 2020 22:47:45: end of X-cor INFO @ Fri, 26 Jun 2020 22:47:45: #2 finished! INFO @ Fri, 26 Jun 2020 22:47:45: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:47:45: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:47:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.05_model.r WARNING @ Fri, 26 Jun 2020 22:47:45: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:47:45: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:47:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:47:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:47:48: 7000000 INFO @ Fri, 26 Jun 2020 22:47:51: 3000000 INFO @ Fri, 26 Jun 2020 22:47:56: 8000000 INFO @ Fri, 26 Jun 2020 22:47:58: 4000000 INFO @ Fri, 26 Jun 2020 22:48:03: 9000000 INFO @ Fri, 26 Jun 2020 22:48:06: 5000000 INFO @ Fri, 26 Jun 2020 22:48:10: 10000000 INFO @ Fri, 26 Jun 2020 22:48:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:48:13: 6000000 INFO @ Fri, 26 Jun 2020 22:48:17: 11000000 INFO @ Fri, 26 Jun 2020 22:48:18: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:48:18: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:48:18: #1 total tags in treatment: 11136177 INFO @ Fri, 26 Jun 2020 22:48:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:48:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:48:19: #1 tags after filtering in treatment: 11136177 INFO @ Fri, 26 Jun 2020 22:48:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:48:19: #1 finished! INFO @ Fri, 26 Jun 2020 22:48:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:48:20: #2 number of paired peaks: 379 WARNING @ Fri, 26 Jun 2020 22:48:20: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Fri, 26 Jun 2020 22:48:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:48:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:48:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:48:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:48:20: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:48:20: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:48:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.10_model.r WARNING @ Fri, 26 Jun 2020 22:48:20: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:48:20: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:48:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:48:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:48:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:48:20: 7000000 INFO @ Fri, 26 Jun 2020 22:48:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:48:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:48:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.05_summits.bed INFO @ Fri, 26 Jun 2020 22:48:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (955 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:48:26: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:48:32: 9000000 INFO @ Fri, 26 Jun 2020 22:48:39: 10000000 INFO @ Fri, 26 Jun 2020 22:48:45: 11000000 INFO @ Fri, 26 Jun 2020 22:48:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:48:46: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:48:46: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:48:46: #1 total tags in treatment: 11136177 INFO @ Fri, 26 Jun 2020 22:48:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:48:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:48:46: #1 tags after filtering in treatment: 11136177 INFO @ Fri, 26 Jun 2020 22:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:48:46: #1 finished! INFO @ Fri, 26 Jun 2020 22:48:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:48:47: #2 number of paired peaks: 379 WARNING @ Fri, 26 Jun 2020 22:48:47: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Fri, 26 Jun 2020 22:48:47: start model_add_line... INFO @ Fri, 26 Jun 2020 22:48:47: start X-correlation... INFO @ Fri, 26 Jun 2020 22:48:47: end of X-cor INFO @ Fri, 26 Jun 2020 22:48:47: #2 finished! INFO @ Fri, 26 Jun 2020 22:48:47: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:48:47: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.20_model.r WARNING @ Fri, 26 Jun 2020 22:48:47: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:48:47: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:48:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:48:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:48:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:48:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:48:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:48:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.10_summits.bed INFO @ Fri, 26 Jun 2020 22:48:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (383 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:49:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:49:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:49:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:49:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495022/SRX495022.20_summits.bed INFO @ Fri, 26 Jun 2020 22:49:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 1 millis CompletedMACS2peakCalling