Job ID = 6507849 SRX = SRX494933 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:41:30 prefetch.2.10.7: 1) Downloading 'SRR1198465'... 2020-06-26T13:41:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:44:02 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:44:02 prefetch.2.10.7: 1) 'SRR1198465' was downloaded successfully Read 23357879 spots for SRR1198465/SRR1198465.sra Written 23357879 spots for SRR1198465/SRR1198465.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: 00:05:07 23357879 reads; of these: 23357879 (100.00%) were unpaired; of these: 1547630 (6.63%) aligned 0 times 18698039 (80.05%) aligned exactly 1 time 3112210 (13.32%) aligned >1 times 93.37% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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] 7257349 / 21810249 = 0.3327 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 22:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.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 22:55:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:55:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:55:55: 1000000 INFO @ Fri, 26 Jun 2020 22:56:00: 2000000 INFO @ Fri, 26 Jun 2020 22:56:06: 3000000 INFO @ Fri, 26 Jun 2020 22:56:11: 4000000 INFO @ Fri, 26 Jun 2020 22:56:16: 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 @ Fri, 26 Jun 2020 22:56:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.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 22:56:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:56:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:56:22: 6000000 INFO @ Fri, 26 Jun 2020 22:56:25: 1000000 INFO @ Fri, 26 Jun 2020 22:56:27: 7000000 INFO @ Fri, 26 Jun 2020 22:56:30: 2000000 INFO @ Fri, 26 Jun 2020 22:56:33: 8000000 INFO @ Fri, 26 Jun 2020 22:56:36: 3000000 INFO @ Fri, 26 Jun 2020 22:56:38: 9000000 INFO @ Fri, 26 Jun 2020 22:56:41: 4000000 INFO @ Fri, 26 Jun 2020 22:56:44: 10000000 INFO @ Fri, 26 Jun 2020 22:56:47: 5000000 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 22:56:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.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 22:56:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:56:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:56:50: 11000000 INFO @ Fri, 26 Jun 2020 22:56:53: 6000000 INFO @ Fri, 26 Jun 2020 22:56:55: 1000000 INFO @ Fri, 26 Jun 2020 22:56:55: 12000000 INFO @ Fri, 26 Jun 2020 22:56:58: 7000000 INFO @ Fri, 26 Jun 2020 22:57:01: 13000000 INFO @ Fri, 26 Jun 2020 22:57:01: 2000000 INFO @ Fri, 26 Jun 2020 22:57:04: 8000000 INFO @ Fri, 26 Jun 2020 22:57:06: 14000000 INFO @ Fri, 26 Jun 2020 22:57:07: 3000000 INFO @ Fri, 26 Jun 2020 22:57:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:57:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:57:10: #1 total tags in treatment: 14552900 INFO @ Fri, 26 Jun 2020 22:57:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:57:10: #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 22:57:10: 9000000 INFO @ Fri, 26 Jun 2020 22:57:10: #1 tags after filtering in treatment: 14552900 INFO @ Fri, 26 Jun 2020 22:57:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:57:10: #1 finished! INFO @ Fri, 26 Jun 2020 22:57:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:57:11: #2 number of paired peaks: 201 WARNING @ Fri, 26 Jun 2020 22:57:11: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Fri, 26 Jun 2020 22:57:11: start model_add_line... INFO @ Fri, 26 Jun 2020 22:57:11: start X-correlation... INFO @ Fri, 26 Jun 2020 22:57:11: end of X-cor INFO @ Fri, 26 Jun 2020 22:57:11: #2 finished! INFO @ Fri, 26 Jun 2020 22:57:11: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:57:11: #2 alternative fragment length(s) may be 2,44,553 bps INFO @ Fri, 26 Jun 2020 22:57:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.05_model.r WARNING @ Fri, 26 Jun 2020 22:57:11: #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 22:57:11: #2 You may need to consider one of the other alternative d(s): 2,44,553 WARNING @ Fri, 26 Jun 2020 22:57:11: #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 22:57:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:57:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:57:12: 4000000 INFO @ Fri, 26 Jun 2020 22:57:15: 10000000 INFO @ Fri, 26 Jun 2020 22:57:18: 5000000 INFO @ Fri, 26 Jun 2020 22:57:21: 11000000 INFO @ Fri, 26 Jun 2020 22:57:23: 6000000 INFO @ Fri, 26 Jun 2020 22:57:27: 12000000 INFO @ Fri, 26 Jun 2020 22:57:29: 7000000 INFO @ Fri, 26 Jun 2020 22:57:32: 13000000 INFO @ Fri, 26 Jun 2020 22:57:34: 8000000 INFO @ Fri, 26 Jun 2020 22:57:38: 14000000 INFO @ Fri, 26 Jun 2020 22:57:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:57:40: 9000000 INFO @ Fri, 26 Jun 2020 22:57:41: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:57:41: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:57:41: #1 total tags in treatment: 14552900 INFO @ Fri, 26 Jun 2020 22:57:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:57:41: #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 22:57:41: #1 tags after filtering in treatment: 14552900 INFO @ Fri, 26 Jun 2020 22:57:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:57:41: #1 finished! INFO @ Fri, 26 Jun 2020 22:57:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:57:42: #2 number of paired peaks: 201 WARNING @ Fri, 26 Jun 2020 22:57:42: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Fri, 26 Jun 2020 22:57:42: start model_add_line... INFO @ Fri, 26 Jun 2020 22:57:42: start X-correlation... INFO @ Fri, 26 Jun 2020 22:57:42: end of X-cor INFO @ Fri, 26 Jun 2020 22:57:42: #2 finished! INFO @ Fri, 26 Jun 2020 22:57:42: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:57:42: #2 alternative fragment length(s) may be 2,44,553 bps INFO @ Fri, 26 Jun 2020 22:57:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.10_model.r WARNING @ Fri, 26 Jun 2020 22:57:42: #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 22:57:42: #2 You may need to consider one of the other alternative d(s): 2,44,553 WARNING @ Fri, 26 Jun 2020 22:57:42: #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 22:57:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:57:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:57:46: 10000000 INFO @ Fri, 26 Jun 2020 22:57:51: 11000000 INFO @ Fri, 26 Jun 2020 22:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:57:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.05_summits.bed INFO @ Fri, 26 Jun 2020 22:57:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (652 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:57:57: 12000000 INFO @ Fri, 26 Jun 2020 22:58:02: 13000000 INFO @ Fri, 26 Jun 2020 22:58:07: 14000000 INFO @ Fri, 26 Jun 2020 22:58:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:58:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:58:10: #1 total tags in treatment: 14552900 INFO @ Fri, 26 Jun 2020 22:58:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:58:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:58:11: #1 tags after filtering in treatment: 14552900 INFO @ Fri, 26 Jun 2020 22:58:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:58:11: #1 finished! INFO @ Fri, 26 Jun 2020 22:58:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:58:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:58:12: #2 number of paired peaks: 201 WARNING @ Fri, 26 Jun 2020 22:58:12: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Fri, 26 Jun 2020 22:58:12: start model_add_line... INFO @ Fri, 26 Jun 2020 22:58:12: start X-correlation... INFO @ Fri, 26 Jun 2020 22:58:12: end of X-cor INFO @ Fri, 26 Jun 2020 22:58:12: #2 finished! INFO @ Fri, 26 Jun 2020 22:58:12: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:58:12: #2 alternative fragment length(s) may be 2,44,553 bps INFO @ Fri, 26 Jun 2020 22:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.20_model.r WARNING @ Fri, 26 Jun 2020 22:58:12: #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 22:58:12: #2 You may need to consider one of the other alternative d(s): 2,44,553 WARNING @ Fri, 26 Jun 2020 22:58:12: #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 22:58:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.10_summits.bed INFO @ Fri, 26 Jun 2020 22:58:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (370 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:58:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494933/SRX494933.20_summits.bed INFO @ Fri, 26 Jun 2020 22:58:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 1 millis CompletedMACS2peakCalling