Job ID = 14157862 SRX = SRX10569198 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T02:45:00 prefetch.2.10.7: 1) Downloading 'SRR14202294'... 2021-12-08T02:45:00 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T03:02:22 prefetch.2.10.7: HTTPS download succeed 2021-12-08T03:02:22 prefetch.2.10.7: 1) 'SRR14202294' was downloaded successfully 2021-12-08T03:02:22 prefetch.2.10.7: 'SRR14202294' has 0 unresolved dependencies Read 22634187 spots for SRR14202294/SRR14202294.sra Written 22634187 spots for SRR14202294/SRR14202294.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158064 ("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: 00:05:08 22634187 reads; of these: 22634187 (100.00%) were unpaired; of these: 12019805 (53.10%) aligned 0 times 8536939 (37.72%) aligned exactly 1 time 2077443 (9.18%) aligned >1 times 46.90% 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 8 files... [bam_rmdupse_core] 2398445 / 10614382 = 0.2260 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 12:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.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 12:12:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:12:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:12:29: 1000000 INFO @ Wed, 08 Dec 2021 12:12:37: 2000000 INFO @ Wed, 08 Dec 2021 12:12:44: 3000000 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 12:12:51: 4000000 INFO @ Wed, 08 Dec 2021 12:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.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 12:12:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:12:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:13:00: 5000000 INFO @ Wed, 08 Dec 2021 12:13:01: 1000000 INFO @ Wed, 08 Dec 2021 12:13:09: 6000000 INFO @ Wed, 08 Dec 2021 12:13:10: 2000000 INFO @ Wed, 08 Dec 2021 12:13:18: 7000000 INFO @ Wed, 08 Dec 2021 12:13:19: 3000000 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 12:13:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.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 12:13:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:13:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:13:26: 8000000 INFO @ Wed, 08 Dec 2021 12:13:28: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 12:13:28: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 12:13:28: #1 total tags in treatment: 8215937 INFO @ Wed, 08 Dec 2021 12:13:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:13:28: #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 12:13:28: #1 tags after filtering in treatment: 8215937 INFO @ Wed, 08 Dec 2021 12:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:13:28: #1 finished! INFO @ Wed, 08 Dec 2021 12:13:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:13:28: 4000000 INFO @ Wed, 08 Dec 2021 12:13:29: #2 number of paired peaks: 228 WARNING @ Wed, 08 Dec 2021 12:13:29: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Wed, 08 Dec 2021 12:13:29: start model_add_line... INFO @ Wed, 08 Dec 2021 12:13:29: start X-correlation... INFO @ Wed, 08 Dec 2021 12:13:29: end of X-cor INFO @ Wed, 08 Dec 2021 12:13:29: #2 finished! INFO @ Wed, 08 Dec 2021 12:13:29: #2 predicted fragment length is 66 bps INFO @ Wed, 08 Dec 2021 12:13:29: #2 alternative fragment length(s) may be 3,66,487,576 bps INFO @ Wed, 08 Dec 2021 12:13:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.05_model.r WARNING @ Wed, 08 Dec 2021 12:13:29: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:13:29: #2 You may need to consider one of the other alternative d(s): 3,66,487,576 WARNING @ Wed, 08 Dec 2021 12:13:29: #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 12:13:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:13:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:13:30: 1000000 INFO @ Wed, 08 Dec 2021 12:13:37: 5000000 INFO @ Wed, 08 Dec 2021 12:13:38: 2000000 INFO @ Wed, 08 Dec 2021 12:13:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:13:46: 3000000 INFO @ Wed, 08 Dec 2021 12:13:47: 6000000 INFO @ Wed, 08 Dec 2021 12:13:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:13:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:13:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.05_summits.bed INFO @ Wed, 08 Dec 2021 12:13:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1152 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:13:55: 4000000 INFO @ Wed, 08 Dec 2021 12:13:56: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:14:03: 5000000 INFO @ Wed, 08 Dec 2021 12:14:05: 8000000 INFO @ Wed, 08 Dec 2021 12:14:07: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 12:14:07: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 12:14:07: #1 total tags in treatment: 8215937 INFO @ Wed, 08 Dec 2021 12:14:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:14:07: #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 12:14:07: #1 tags after filtering in treatment: 8215937 INFO @ Wed, 08 Dec 2021 12:14:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:14:07: #1 finished! INFO @ Wed, 08 Dec 2021 12:14:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:14:07: #2 number of paired peaks: 228 WARNING @ Wed, 08 Dec 2021 12:14:07: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Wed, 08 Dec 2021 12:14:07: start model_add_line... INFO @ Wed, 08 Dec 2021 12:14:08: start X-correlation... INFO @ Wed, 08 Dec 2021 12:14:08: end of X-cor INFO @ Wed, 08 Dec 2021 12:14:08: #2 finished! INFO @ Wed, 08 Dec 2021 12:14:08: #2 predicted fragment length is 66 bps INFO @ Wed, 08 Dec 2021 12:14:08: #2 alternative fragment length(s) may be 3,66,487,576 bps INFO @ Wed, 08 Dec 2021 12:14:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.10_model.r WARNING @ Wed, 08 Dec 2021 12:14:08: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:14:08: #2 You may need to consider one of the other alternative d(s): 3,66,487,576 WARNING @ Wed, 08 Dec 2021 12:14:08: #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 12:14:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:14:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:14:11: 6000000 INFO @ Wed, 08 Dec 2021 12:14:18: 7000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:14:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:14:26: 8000000 INFO @ Wed, 08 Dec 2021 12:14:27: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 12:14:27: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 12:14:27: #1 total tags in treatment: 8215937 INFO @ Wed, 08 Dec 2021 12:14:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:14:27: #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 12:14:27: #1 tags after filtering in treatment: 8215937 INFO @ Wed, 08 Dec 2021 12:14:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:14:27: #1 finished! INFO @ Wed, 08 Dec 2021 12:14:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:14:28: #2 number of paired peaks: 228 WARNING @ Wed, 08 Dec 2021 12:14:28: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Wed, 08 Dec 2021 12:14:28: start model_add_line... INFO @ Wed, 08 Dec 2021 12:14:28: start X-correlation... INFO @ Wed, 08 Dec 2021 12:14:28: end of X-cor INFO @ Wed, 08 Dec 2021 12:14:28: #2 finished! INFO @ Wed, 08 Dec 2021 12:14:28: #2 predicted fragment length is 66 bps INFO @ Wed, 08 Dec 2021 12:14:28: #2 alternative fragment length(s) may be 3,66,487,576 bps INFO @ Wed, 08 Dec 2021 12:14:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.20_model.r WARNING @ Wed, 08 Dec 2021 12:14:28: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:14:28: #2 You may need to consider one of the other alternative d(s): 3,66,487,576 WARNING @ Wed, 08 Dec 2021 12:14:28: #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 12:14:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:14:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:14:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:14:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.10_summits.bed INFO @ Wed, 08 Dec 2021 12:14:31: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (308 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:14:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:14:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:14:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:14:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569198/SRX10569198.20_summits.bed INFO @ Wed, 08 Dec 2021 12:14:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 1 millis CompletedMACS2peakCalling