Job ID = 14159599 SRX = SRX3180778 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20986887 spots for SRR6030429/SRR6030429.sra Written 20986887 spots for SRR6030429/SRR6030429.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160110 ("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: 00:04:29 20986887 reads; of these: 20986887 (100.00%) were unpaired; of these: 449867 (2.14%) aligned 0 times 16645283 (79.31%) aligned exactly 1 time 3891737 (18.54%) aligned >1 times 97.86% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 3714434 / 20537020 = 0.1809 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 23:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.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 @ Wed, 08 Dec 2021 23:24:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:24:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:24:21: 1000000 INFO @ Wed, 08 Dec 2021 23:24:27: 2000000 INFO @ Wed, 08 Dec 2021 23:24:32: 3000000 INFO @ Wed, 08 Dec 2021 23:24:38: 4000000 INFO @ Wed, 08 Dec 2021 23:24:43: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 23:24:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.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 @ Wed, 08 Dec 2021 23:24:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:24:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:24:49: 6000000 INFO @ Wed, 08 Dec 2021 23:24:50: 1000000 INFO @ Wed, 08 Dec 2021 23:24:55: 7000000 INFO @ Wed, 08 Dec 2021 23:24:55: 2000000 INFO @ Wed, 08 Dec 2021 23:25:00: 3000000 INFO @ Wed, 08 Dec 2021 23:25:01: 8000000 INFO @ Wed, 08 Dec 2021 23:25:05: 4000000 INFO @ Wed, 08 Dec 2021 23:25:07: 9000000 INFO @ Wed, 08 Dec 2021 23:25:10: 5000000 INFO @ Wed, 08 Dec 2021 23:25:12: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 23:25:15: 6000000 INFO @ Wed, 08 Dec 2021 23:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.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 @ Wed, 08 Dec 2021 23:25:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:25:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:25:18: 11000000 INFO @ Wed, 08 Dec 2021 23:25:20: 7000000 INFO @ Wed, 08 Dec 2021 23:25:20: 1000000 INFO @ Wed, 08 Dec 2021 23:25:24: 12000000 INFO @ Wed, 08 Dec 2021 23:25:25: 8000000 INFO @ Wed, 08 Dec 2021 23:25:25: 2000000 INFO @ Wed, 08 Dec 2021 23:25:29: 13000000 INFO @ Wed, 08 Dec 2021 23:25:30: 9000000 INFO @ Wed, 08 Dec 2021 23:25:30: 3000000 INFO @ Wed, 08 Dec 2021 23:25:35: 14000000 INFO @ Wed, 08 Dec 2021 23:25:35: 10000000 INFO @ Wed, 08 Dec 2021 23:25:35: 4000000 INFO @ Wed, 08 Dec 2021 23:25:40: 11000000 INFO @ Wed, 08 Dec 2021 23:25:40: 5000000 INFO @ Wed, 08 Dec 2021 23:25:41: 15000000 INFO @ Wed, 08 Dec 2021 23:25:45: 12000000 INFO @ Wed, 08 Dec 2021 23:25:45: 6000000 INFO @ Wed, 08 Dec 2021 23:25:46: 16000000 INFO @ Wed, 08 Dec 2021 23:25:50: 13000000 INFO @ Wed, 08 Dec 2021 23:25:50: 7000000 INFO @ Wed, 08 Dec 2021 23:25:51: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:25:51: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:25:51: #1 total tags in treatment: 16822586 INFO @ Wed, 08 Dec 2021 23:25:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:25:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:25:51: #1 tags after filtering in treatment: 16822586 INFO @ Wed, 08 Dec 2021 23:25:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:25:51: #1 finished! INFO @ Wed, 08 Dec 2021 23:25:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:25:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:25:52: #2 number of paired peaks: 363 WARNING @ Wed, 08 Dec 2021 23:25:52: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Wed, 08 Dec 2021 23:25:52: start model_add_line... INFO @ Wed, 08 Dec 2021 23:25:53: start X-correlation... INFO @ Wed, 08 Dec 2021 23:25:53: end of X-cor INFO @ Wed, 08 Dec 2021 23:25:53: #2 finished! INFO @ Wed, 08 Dec 2021 23:25:53: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:25:53: #2 alternative fragment length(s) may be 1,48,531,567 bps INFO @ Wed, 08 Dec 2021 23:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.05_model.r WARNING @ Wed, 08 Dec 2021 23:25:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:25:53: #2 You may need to consider one of the other alternative d(s): 1,48,531,567 WARNING @ Wed, 08 Dec 2021 23:25:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:25:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:25:55: 14000000 INFO @ Wed, 08 Dec 2021 23:25:55: 8000000 INFO @ Wed, 08 Dec 2021 23:26:00: 15000000 INFO @ Wed, 08 Dec 2021 23:26:00: 9000000 INFO @ Wed, 08 Dec 2021 23:26:05: 16000000 INFO @ Wed, 08 Dec 2021 23:26:05: 10000000 INFO @ Wed, 08 Dec 2021 23:26:09: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:26:09: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:26:09: #1 total tags in treatment: 16822586 INFO @ Wed, 08 Dec 2021 23:26:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:26:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:26:09: #1 tags after filtering in treatment: 16822586 INFO @ Wed, 08 Dec 2021 23:26:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:26:09: #1 finished! INFO @ Wed, 08 Dec 2021 23:26:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:26:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:26:10: 11000000 INFO @ Wed, 08 Dec 2021 23:26:10: #2 number of paired peaks: 363 WARNING @ Wed, 08 Dec 2021 23:26:10: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Wed, 08 Dec 2021 23:26:10: start model_add_line... INFO @ Wed, 08 Dec 2021 23:26:11: start X-correlation... INFO @ Wed, 08 Dec 2021 23:26:11: end of X-cor INFO @ Wed, 08 Dec 2021 23:26:11: #2 finished! INFO @ Wed, 08 Dec 2021 23:26:11: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:26:11: #2 alternative fragment length(s) may be 1,48,531,567 bps INFO @ Wed, 08 Dec 2021 23:26:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.10_model.r WARNING @ Wed, 08 Dec 2021 23:26:11: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:26:11: #2 You may need to consider one of the other alternative d(s): 1,48,531,567 WARNING @ Wed, 08 Dec 2021 23:26:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:26:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:26:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:26:15: 12000000 INFO @ Wed, 08 Dec 2021 23:26:20: 13000000 INFO @ Wed, 08 Dec 2021 23:26:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:26:24: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:26:29: 15000000 INFO @ Wed, 08 Dec 2021 23:26:34: 16000000 INFO @ Wed, 08 Dec 2021 23:26:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:26:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:26:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.05_summits.bed INFO @ Wed, 08 Dec 2021 23:26:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (771 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:26:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:26:38: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:26:38: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:26:38: #1 total tags in treatment: 16822586 INFO @ Wed, 08 Dec 2021 23:26:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:26:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:26:38: #1 tags after filtering in treatment: 16822586 INFO @ Wed, 08 Dec 2021 23:26:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:26:38: #1 finished! INFO @ Wed, 08 Dec 2021 23:26:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:26:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:26:39: #2 number of paired peaks: 363 WARNING @ Wed, 08 Dec 2021 23:26:39: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Wed, 08 Dec 2021 23:26:39: start model_add_line... INFO @ Wed, 08 Dec 2021 23:26:40: start X-correlation... INFO @ Wed, 08 Dec 2021 23:26:40: end of X-cor INFO @ Wed, 08 Dec 2021 23:26:40: #2 finished! INFO @ Wed, 08 Dec 2021 23:26:40: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 23:26:40: #2 alternative fragment length(s) may be 1,48,531,567 bps INFO @ Wed, 08 Dec 2021 23:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.20_model.r WARNING @ Wed, 08 Dec 2021 23:26:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:26:40: #2 You may need to consider one of the other alternative d(s): 1,48,531,567 WARNING @ Wed, 08 Dec 2021 23:26:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:26:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.10_summits.bed INFO @ Wed, 08 Dec 2021 23:26:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (519 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:27:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180778/SRX3180778.20_summits.bed INFO @ Wed, 08 Dec 2021 23:27:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 1 millis CompletedMACS2peakCalling