Job ID = 10165628 SRX = SRX6799185 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34054065 spots for SRR10065392/SRR10065392.sra Written 34054065 spots for SRR10065392/SRR10065392.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165886 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:25 34054065 reads; of these: 34054065 (100.00%) were unpaired; of these: 2235614 (6.56%) aligned 0 times 24303183 (71.37%) aligned exactly 1 time 7515268 (22.07%) aligned >1 times 93.44% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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 16 files... [bam_rmdupse_core] 8936797 / 31818451 = 0.2809 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 @ Thu, 08 Oct 2020 19:46:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.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 @ Thu, 08 Oct 2020 19:46:17: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:17: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:46:21: 1000000 INFO @ Thu, 08 Oct 2020 19:46:26: 2000000 INFO @ Thu, 08 Oct 2020 19:46:31: 3000000 INFO @ Thu, 08 Oct 2020 19:46:35: 4000000 INFO @ Thu, 08 Oct 2020 19:46:40: 5000000 INFO @ Thu, 08 Oct 2020 19:46:44: 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 @ Thu, 08 Oct 2020 19:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.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 @ Thu, 08 Oct 2020 19:46:46: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:46: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:46:49: 7000000 INFO @ Thu, 08 Oct 2020 19:46:51: 1000000 INFO @ Thu, 08 Oct 2020 19:46:54: 8000000 INFO @ Thu, 08 Oct 2020 19:46:56: 2000000 INFO @ Thu, 08 Oct 2020 19:46:59: 9000000 INFO @ Thu, 08 Oct 2020 19:47:01: 3000000 INFO @ Thu, 08 Oct 2020 19:47:04: 10000000 INFO @ Thu, 08 Oct 2020 19:47:06: 4000000 INFO @ Thu, 08 Oct 2020 19:47:08: 11000000 INFO @ Thu, 08 Oct 2020 19:47:11: 5000000 INFO @ Thu, 08 Oct 2020 19:47:13: 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 @ Thu, 08 Oct 2020 19:47:16: 6000000 INFO @ Thu, 08 Oct 2020 19:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.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 @ Thu, 08 Oct 2020 19:47:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:18: 13000000 INFO @ Thu, 08 Oct 2020 19:47:21: 7000000 INFO @ Thu, 08 Oct 2020 19:47:21: 1000000 INFO @ Thu, 08 Oct 2020 19:47:23: 14000000 INFO @ Thu, 08 Oct 2020 19:47:26: 8000000 INFO @ Thu, 08 Oct 2020 19:47:26: 2000000 INFO @ Thu, 08 Oct 2020 19:47:28: 15000000 INFO @ Thu, 08 Oct 2020 19:47:31: 9000000 INFO @ Thu, 08 Oct 2020 19:47:31: 3000000 INFO @ Thu, 08 Oct 2020 19:47:33: 16000000 INFO @ Thu, 08 Oct 2020 19:47:36: 10000000 INFO @ Thu, 08 Oct 2020 19:47:36: 4000000 INFO @ Thu, 08 Oct 2020 19:47:38: 17000000 INFO @ Thu, 08 Oct 2020 19:47:41: 11000000 INFO @ Thu, 08 Oct 2020 19:47:41: 5000000 INFO @ Thu, 08 Oct 2020 19:47:43: 18000000 INFO @ Thu, 08 Oct 2020 19:47:46: 12000000 INFO @ Thu, 08 Oct 2020 19:47:46: 6000000 INFO @ Thu, 08 Oct 2020 19:47:48: 19000000 INFO @ Thu, 08 Oct 2020 19:47:51: 13000000 INFO @ Thu, 08 Oct 2020 19:47:51: 7000000 INFO @ Thu, 08 Oct 2020 19:47:53: 20000000 INFO @ Thu, 08 Oct 2020 19:47:56: 14000000 INFO @ Thu, 08 Oct 2020 19:47:56: 8000000 INFO @ Thu, 08 Oct 2020 19:47:58: 21000000 INFO @ Thu, 08 Oct 2020 19:48:00: 15000000 INFO @ Thu, 08 Oct 2020 19:48:01: 9000000 INFO @ Thu, 08 Oct 2020 19:48:03: 22000000 INFO @ Thu, 08 Oct 2020 19:48:05: 16000000 INFO @ Thu, 08 Oct 2020 19:48:06: 10000000 INFO @ Thu, 08 Oct 2020 19:48:07: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:48:07: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:48:07: #1 total tags in treatment: 22881654 INFO @ Thu, 08 Oct 2020 19:48:07: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:48:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:48:08: #1 tags after filtering in treatment: 22881654 INFO @ Thu, 08 Oct 2020 19:48:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:48:08: #1 finished! INFO @ Thu, 08 Oct 2020 19:48:08: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:48:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:48:09: #2 number of paired peaks: 219 WARNING @ Thu, 08 Oct 2020 19:48:09: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Thu, 08 Oct 2020 19:48:09: start model_add_line... INFO @ Thu, 08 Oct 2020 19:48:09: start X-correlation... INFO @ Thu, 08 Oct 2020 19:48:09: end of X-cor INFO @ Thu, 08 Oct 2020 19:48:09: #2 finished! INFO @ Thu, 08 Oct 2020 19:48:09: #2 predicted fragment length is 59 bps INFO @ Thu, 08 Oct 2020 19:48:09: #2 alternative fragment length(s) may be 2,49,59,85 bps INFO @ Thu, 08 Oct 2020 19:48:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05_model.r WARNING @ Thu, 08 Oct 2020 19:48:09: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:48:09: #2 You may need to consider one of the other alternative d(s): 2,49,59,85 WARNING @ Thu, 08 Oct 2020 19:48:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:48:09: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:48:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:48:10: 17000000 INFO @ Thu, 08 Oct 2020 19:48:11: 11000000 INFO @ Thu, 08 Oct 2020 19:48:15: 18000000 INFO @ Thu, 08 Oct 2020 19:48:15: 12000000 INFO @ Thu, 08 Oct 2020 19:48:20: 19000000 INFO @ Thu, 08 Oct 2020 19:48:20: 13000000 INFO @ Thu, 08 Oct 2020 19:48:25: 14000000 INFO @ Thu, 08 Oct 2020 19:48:25: 20000000 INFO @ Thu, 08 Oct 2020 19:48:30: 15000000 INFO @ Thu, 08 Oct 2020 19:48:30: 21000000 INFO @ Thu, 08 Oct 2020 19:48:35: 16000000 INFO @ Thu, 08 Oct 2020 19:48:35: 22000000 INFO @ Thu, 08 Oct 2020 19:48:40: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:48:40: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:48:40: #1 total tags in treatment: 22881654 INFO @ Thu, 08 Oct 2020 19:48:40: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:48:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:48:40: 17000000 INFO @ Thu, 08 Oct 2020 19:48:40: #1 tags after filtering in treatment: 22881654 INFO @ Thu, 08 Oct 2020 19:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:48:40: #1 finished! INFO @ Thu, 08 Oct 2020 19:48:40: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:48:41: #2 number of paired peaks: 219 WARNING @ Thu, 08 Oct 2020 19:48:41: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Thu, 08 Oct 2020 19:48:41: start model_add_line... INFO @ Thu, 08 Oct 2020 19:48:41: start X-correlation... INFO @ Thu, 08 Oct 2020 19:48:41: end of X-cor INFO @ Thu, 08 Oct 2020 19:48:41: #2 finished! INFO @ Thu, 08 Oct 2020 19:48:41: #2 predicted fragment length is 59 bps INFO @ Thu, 08 Oct 2020 19:48:41: #2 alternative fragment length(s) may be 2,49,59,85 bps INFO @ Thu, 08 Oct 2020 19:48:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10_model.r WARNING @ Thu, 08 Oct 2020 19:48:41: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:48:41: #2 You may need to consider one of the other alternative d(s): 2,49,59,85 WARNING @ Thu, 08 Oct 2020 19:48:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:48:41: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:48:45: 18000000 INFO @ Thu, 08 Oct 2020 19:48:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:48:50: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:48:54: 20000000 INFO @ Thu, 08 Oct 2020 19:48:59: 21000000 INFO @ Thu, 08 Oct 2020 19:49:04: 22000000 INFO @ Thu, 08 Oct 2020 19:49:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:49:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:49:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.05_summits.bed INFO @ Thu, 08 Oct 2020 19:49:08: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9793 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:49:08: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:49:08: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:49:08: #1 total tags in treatment: 22881654 INFO @ Thu, 08 Oct 2020 19:49:08: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:49:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:49:09: #1 tags after filtering in treatment: 22881654 INFO @ Thu, 08 Oct 2020 19:49:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:49:09: #1 finished! INFO @ Thu, 08 Oct 2020 19:49:09: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:49:10: #2 number of paired peaks: 219 WARNING @ Thu, 08 Oct 2020 19:49:10: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Thu, 08 Oct 2020 19:49:10: start model_add_line... INFO @ Thu, 08 Oct 2020 19:49:10: start X-correlation... INFO @ Thu, 08 Oct 2020 19:49:10: end of X-cor INFO @ Thu, 08 Oct 2020 19:49:10: #2 finished! INFO @ Thu, 08 Oct 2020 19:49:10: #2 predicted fragment length is 59 bps INFO @ Thu, 08 Oct 2020 19:49:10: #2 alternative fragment length(s) may be 2,49,59,85 bps INFO @ Thu, 08 Oct 2020 19:49:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20_model.r WARNING @ Thu, 08 Oct 2020 19:49:10: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:49:10: #2 You may need to consider one of the other alternative d(s): 2,49,59,85 WARNING @ Thu, 08 Oct 2020 19:49:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:49:10: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:49:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:49:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:49:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:49:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.10_summits.bed INFO @ Thu, 08 Oct 2020 19:49:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3248 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:49:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799185/SRX6799185.20_summits.bed INFO @ Thu, 08 Oct 2020 19:50:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (485 records, 4 fields): 2 millis CompletedMACS2peakCalling