Job ID = 14159270 SRX = SRX3180814 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20542845 spots for SRR6030465/SRR6030465.sra Written 20542845 spots for SRR6030465/SRR6030465.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159485 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:31 20542845 reads; of these: 20542845 (100.00%) were unpaired; of these: 783802 (3.82%) aligned 0 times 16187024 (78.80%) aligned exactly 1 time 3572019 (17.39%) aligned >1 times 96.18% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 4663117 / 19759043 = 0.2360 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 20:44:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.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 20:44:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:44:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:44:22: 1000000 INFO @ Wed, 08 Dec 2021 20:44:29: 2000000 INFO @ Wed, 08 Dec 2021 20:44:35: 3000000 INFO @ Wed, 08 Dec 2021 20:44:41: 4000000 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 20:44:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.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 20:44:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:44:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:44:47: 5000000 INFO @ Wed, 08 Dec 2021 20:44:53: 1000000 INFO @ Wed, 08 Dec 2021 20:44:54: 6000000 INFO @ Wed, 08 Dec 2021 20:45:00: 2000000 INFO @ Wed, 08 Dec 2021 20:45:00: 7000000 INFO @ Wed, 08 Dec 2021 20:45:06: 3000000 INFO @ Wed, 08 Dec 2021 20:45:07: 8000000 INFO @ Wed, 08 Dec 2021 20:45:13: 9000000 INFO @ Wed, 08 Dec 2021 20:45:13: 4000000 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 20:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.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 20:45:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:45:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:45:19: 10000000 INFO @ Wed, 08 Dec 2021 20:45:20: 5000000 INFO @ Wed, 08 Dec 2021 20:45:23: 1000000 INFO @ Wed, 08 Dec 2021 20:45:26: 11000000 INFO @ Wed, 08 Dec 2021 20:45:27: 6000000 INFO @ Wed, 08 Dec 2021 20:45:29: 2000000 INFO @ Wed, 08 Dec 2021 20:45:32: 12000000 INFO @ Wed, 08 Dec 2021 20:45:34: 7000000 INFO @ Wed, 08 Dec 2021 20:45:36: 3000000 INFO @ Wed, 08 Dec 2021 20:45:39: 13000000 INFO @ Wed, 08 Dec 2021 20:45:40: 8000000 INFO @ Wed, 08 Dec 2021 20:45:42: 4000000 INFO @ Wed, 08 Dec 2021 20:45:45: 14000000 INFO @ Wed, 08 Dec 2021 20:45:47: 9000000 INFO @ Wed, 08 Dec 2021 20:45:48: 5000000 INFO @ Wed, 08 Dec 2021 20:45:52: 15000000 INFO @ Wed, 08 Dec 2021 20:45:52: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:45:52: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:45:52: #1 total tags in treatment: 15095926 INFO @ Wed, 08 Dec 2021 20:45:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:45:52: #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 20:45:53: #1 tags after filtering in treatment: 15095926 INFO @ Wed, 08 Dec 2021 20:45:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:45:53: #1 finished! INFO @ Wed, 08 Dec 2021 20:45:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:45:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:45:54: #2 number of paired peaks: 376 WARNING @ Wed, 08 Dec 2021 20:45:54: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Wed, 08 Dec 2021 20:45:54: start model_add_line... INFO @ Wed, 08 Dec 2021 20:45:54: start X-correlation... INFO @ Wed, 08 Dec 2021 20:45:54: end of X-cor INFO @ Wed, 08 Dec 2021 20:45:54: #2 finished! INFO @ Wed, 08 Dec 2021 20:45:54: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:45:54: #2 alternative fragment length(s) may be 1,35,530,552 bps INFO @ Wed, 08 Dec 2021 20:45:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.05_model.r WARNING @ Wed, 08 Dec 2021 20:45:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:45:54: #2 You may need to consider one of the other alternative d(s): 1,35,530,552 WARNING @ Wed, 08 Dec 2021 20:45:54: #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 20:45:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:45:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:45:54: 10000000 INFO @ Wed, 08 Dec 2021 20:45:55: 6000000 INFO @ Wed, 08 Dec 2021 20:46:01: 11000000 INFO @ Wed, 08 Dec 2021 20:46:02: 7000000 INFO @ Wed, 08 Dec 2021 20:46:08: 12000000 INFO @ Wed, 08 Dec 2021 20:46:08: 8000000 INFO @ Wed, 08 Dec 2021 20:46:15: 13000000 INFO @ Wed, 08 Dec 2021 20:46:15: 9000000 INFO @ Wed, 08 Dec 2021 20:46:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:46:21: 14000000 INFO @ Wed, 08 Dec 2021 20:46:22: 10000000 INFO @ Wed, 08 Dec 2021 20:46:28: 15000000 INFO @ Wed, 08 Dec 2021 20:46:28: 11000000 INFO @ Wed, 08 Dec 2021 20:46:29: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:46:29: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:46:29: #1 total tags in treatment: 15095926 INFO @ Wed, 08 Dec 2021 20:46:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:46:29: #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 20:46:29: #1 tags after filtering in treatment: 15095926 INFO @ Wed, 08 Dec 2021 20:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:46:29: #1 finished! INFO @ Wed, 08 Dec 2021 20:46:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:46:30: #2 number of paired peaks: 376 WARNING @ Wed, 08 Dec 2021 20:46:30: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Wed, 08 Dec 2021 20:46:30: start model_add_line... INFO @ Wed, 08 Dec 2021 20:46:30: start X-correlation... INFO @ Wed, 08 Dec 2021 20:46:30: end of X-cor INFO @ Wed, 08 Dec 2021 20:46:30: #2 finished! INFO @ Wed, 08 Dec 2021 20:46:30: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:46:30: #2 alternative fragment length(s) may be 1,35,530,552 bps INFO @ Wed, 08 Dec 2021 20:46:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.10_model.r WARNING @ Wed, 08 Dec 2021 20:46:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:46:30: #2 You may need to consider one of the other alternative d(s): 1,35,530,552 WARNING @ Wed, 08 Dec 2021 20:46:30: #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 20:46:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:46:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:46:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:46:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:46:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.05_summits.bed INFO @ Wed, 08 Dec 2021 20:46:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:46:35: 12000000 INFO @ Wed, 08 Dec 2021 20:46:41: 13000000 INFO @ Wed, 08 Dec 2021 20:46:47: 14000000 INFO @ Wed, 08 Dec 2021 20:46:53: 15000000 INFO @ Wed, 08 Dec 2021 20:46:53: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:46:53: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:46:53: #1 total tags in treatment: 15095926 INFO @ Wed, 08 Dec 2021 20:46:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:46:53: #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 20:46:54: #1 tags after filtering in treatment: 15095926 INFO @ Wed, 08 Dec 2021 20:46:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:46:54: #1 finished! INFO @ Wed, 08 Dec 2021 20:46:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:46:55: #2 number of paired peaks: 376 WARNING @ Wed, 08 Dec 2021 20:46:55: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Wed, 08 Dec 2021 20:46:55: start model_add_line... INFO @ Wed, 08 Dec 2021 20:46:55: start X-correlation... INFO @ Wed, 08 Dec 2021 20:46:55: end of X-cor INFO @ Wed, 08 Dec 2021 20:46:55: #2 finished! INFO @ Wed, 08 Dec 2021 20:46:55: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:46:55: #2 alternative fragment length(s) may be 1,35,530,552 bps INFO @ Wed, 08 Dec 2021 20:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.20_model.r WARNING @ Wed, 08 Dec 2021 20:46:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:46:55: #2 You may need to consider one of the other alternative d(s): 1,35,530,552 WARNING @ Wed, 08 Dec 2021 20:46:55: #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 20:46:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:46:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:47:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:47:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:47:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.10_summits.bed INFO @ Wed, 08 Dec 2021 20:47:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:47:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180814/SRX3180814.20_summits.bed INFO @ Wed, 08 Dec 2021 20:47:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling