Job ID = 10165664 SRX = SRX7879267 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29956757 spots for SRR11272882/SRR11272882.sra Written 29956757 spots for SRR11272882/SRR11272882.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165864 ("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: 00:04:58 29956757 reads; of these: 29956757 (100.00%) were unpaired; of these: 8822368 (29.45%) aligned 0 times 17733149 (59.20%) aligned exactly 1 time 3401240 (11.35%) aligned >1 times 70.55% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 11245525 / 21134389 = 0.5321 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 19:42:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.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 19:42:54: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:42:54: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:42:59: 1000000 INFO @ Thu, 08 Oct 2020 19:43:04: 2000000 INFO @ Thu, 08 Oct 2020 19:43:09: 3000000 INFO @ Thu, 08 Oct 2020 19:43:14: 4000000 INFO @ Thu, 08 Oct 2020 19:43:19: 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 @ Thu, 08 Oct 2020 19:43:24: 6000000 INFO @ Thu, 08 Oct 2020 19:43:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.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 19:43:24: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:43:24: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:43:30: 7000000 INFO @ Thu, 08 Oct 2020 19:43:30: 1000000 INFO @ Thu, 08 Oct 2020 19:43:35: 8000000 INFO @ Thu, 08 Oct 2020 19:43:35: 2000000 INFO @ Thu, 08 Oct 2020 19:43:40: 9000000 INFO @ Thu, 08 Oct 2020 19:43:41: 3000000 INFO @ Thu, 08 Oct 2020 19:43:45: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:43:45: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:43:45: #1 total tags in treatment: 9888864 INFO @ Thu, 08 Oct 2020 19:43:45: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:43:45: #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 19:43:45: #1 tags after filtering in treatment: 9888864 INFO @ Thu, 08 Oct 2020 19:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:43:45: #1 finished! INFO @ Thu, 08 Oct 2020 19:43:45: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:43:46: 4000000 INFO @ Thu, 08 Oct 2020 19:43:46: #2 number of paired peaks: 434 WARNING @ Thu, 08 Oct 2020 19:43:46: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Thu, 08 Oct 2020 19:43:46: start model_add_line... INFO @ Thu, 08 Oct 2020 19:43:46: start X-correlation... INFO @ Thu, 08 Oct 2020 19:43:46: end of X-cor INFO @ Thu, 08 Oct 2020 19:43:46: #2 finished! INFO @ Thu, 08 Oct 2020 19:43:46: #2 predicted fragment length is 48 bps INFO @ Thu, 08 Oct 2020 19:43:46: #2 alternative fragment length(s) may be 2,48,546 bps INFO @ Thu, 08 Oct 2020 19:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.05_model.r WARNING @ Thu, 08 Oct 2020 19:43:46: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:43:46: #2 You may need to consider one of the other alternative d(s): 2,48,546 WARNING @ Thu, 08 Oct 2020 19:43:46: #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 19:43:46: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:43:46: #3 Pre-compute pvalue-qvalue table... 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 19:43:51: 5000000 INFO @ Thu, 08 Oct 2020 19:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.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 19:43:55: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:43:55: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:43:56: 6000000 INFO @ Thu, 08 Oct 2020 19:44:01: 1000000 INFO @ Thu, 08 Oct 2020 19:44:02: 7000000 INFO @ Thu, 08 Oct 2020 19:44:06: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:44:07: 2000000 INFO @ Thu, 08 Oct 2020 19:44:08: 8000000 INFO @ Thu, 08 Oct 2020 19:44:13: 3000000 INFO @ Thu, 08 Oct 2020 19:44:13: 9000000 INFO @ Thu, 08 Oct 2020 19:44:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:44:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:44:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.05_summits.bed INFO @ Thu, 08 Oct 2020 19:44:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (767 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:44:18: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:44:18: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:44:18: #1 total tags in treatment: 9888864 INFO @ Thu, 08 Oct 2020 19:44:18: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:44:18: #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 19:44:18: #1 tags after filtering in treatment: 9888864 INFO @ Thu, 08 Oct 2020 19:44:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:44:18: #1 finished! INFO @ Thu, 08 Oct 2020 19:44:18: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:44:19: 4000000 INFO @ Thu, 08 Oct 2020 19:44:19: #2 number of paired peaks: 434 WARNING @ Thu, 08 Oct 2020 19:44:19: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Thu, 08 Oct 2020 19:44:19: start model_add_line... INFO @ Thu, 08 Oct 2020 19:44:19: start X-correlation... INFO @ Thu, 08 Oct 2020 19:44:19: end of X-cor INFO @ Thu, 08 Oct 2020 19:44:19: #2 finished! INFO @ Thu, 08 Oct 2020 19:44:19: #2 predicted fragment length is 48 bps INFO @ Thu, 08 Oct 2020 19:44:19: #2 alternative fragment length(s) may be 2,48,546 bps INFO @ Thu, 08 Oct 2020 19:44:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.10_model.r WARNING @ Thu, 08 Oct 2020 19:44:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:44:19: #2 You may need to consider one of the other alternative d(s): 2,48,546 WARNING @ Thu, 08 Oct 2020 19:44:19: #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 19:44:19: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:44:25: 5000000 INFO @ Thu, 08 Oct 2020 19:44:30: 6000000 INFO @ Thu, 08 Oct 2020 19:44:36: 7000000 INFO @ Thu, 08 Oct 2020 19:44:39: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:44:42: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:44:47: 9000000 INFO @ Thu, 08 Oct 2020 19:44:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:44:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:44:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.10_summits.bed INFO @ Thu, 08 Oct 2020 19:44:49: Done! INFO @ Thu, 08 Oct 2020 19:44:53: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:44:53: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:44:53: #1 total tags in treatment: 9888864 INFO @ Thu, 08 Oct 2020 19:44:53: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:44:53: #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 19:44:53: #1 tags after filtering in treatment: 9888864 INFO @ Thu, 08 Oct 2020 19:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:44:53: #1 finished! INFO @ Thu, 08 Oct 2020 19:44:53: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:44:53: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:44:54: #2 number of paired peaks: 434 WARNING @ Thu, 08 Oct 2020 19:44:54: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Thu, 08 Oct 2020 19:44:54: start model_add_line... INFO @ Thu, 08 Oct 2020 19:44:54: start X-correlation... INFO @ Thu, 08 Oct 2020 19:44:54: end of X-cor INFO @ Thu, 08 Oct 2020 19:44:54: #2 finished! INFO @ Thu, 08 Oct 2020 19:44:54: #2 predicted fragment length is 48 bps INFO @ Thu, 08 Oct 2020 19:44:54: #2 alternative fragment length(s) may be 2,48,546 bps INFO @ Thu, 08 Oct 2020 19:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.20_model.r WARNING @ Thu, 08 Oct 2020 19:44:54: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:44:54: #2 You may need to consider one of the other alternative d(s): 2,48,546 WARNING @ Thu, 08 Oct 2020 19:44:54: #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 19:44:54: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:44:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:45:12: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:45:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:45:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:45:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879267/SRX7879267.20_summits.bed INFO @ Thu, 08 Oct 2020 19:45:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 1 millis CompletedMACS2peakCalling