Job ID = 14160561 SRX = SRX10399008 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10237567 spots for SRR14022396/SRR14022396.sra Written 10237567 spots for SRR14022396/SRR14022396.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160684 ("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: 00:02:43 10237567 reads; of these: 10237567 (100.00%) were unpaired; of these: 101315 (0.99%) aligned 0 times 8413901 (82.19%) aligned exactly 1 time 1722351 (16.82%) aligned >1 times 99.01% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 742107 / 10136252 = 0.0732 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 @ Thu, 09 Dec 2021 03:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.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, 09 Dec 2021 03:18:54: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:18:54: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:19:05: 1000000 INFO @ Thu, 09 Dec 2021 03:19:15: 2000000 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 @ Thu, 09 Dec 2021 03:19:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.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, 09 Dec 2021 03:19:23: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:19:23: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:19:26: 3000000 INFO @ Thu, 09 Dec 2021 03:19:33: 1000000 INFO @ Thu, 09 Dec 2021 03:19:37: 4000000 INFO @ Thu, 09 Dec 2021 03:19:42: 2000000 INFO @ Thu, 09 Dec 2021 03:19:48: 5000000 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 @ Thu, 09 Dec 2021 03:19:52: 3000000 INFO @ Thu, 09 Dec 2021 03:19:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.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, 09 Dec 2021 03:19:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:19:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:19:59: 6000000 INFO @ Thu, 09 Dec 2021 03:20:01: 4000000 INFO @ Thu, 09 Dec 2021 03:20:02: 1000000 INFO @ Thu, 09 Dec 2021 03:20:09: 7000000 INFO @ Thu, 09 Dec 2021 03:20:11: 5000000 INFO @ Thu, 09 Dec 2021 03:20:11: 2000000 INFO @ Thu, 09 Dec 2021 03:20:20: 8000000 INFO @ Thu, 09 Dec 2021 03:20:20: 3000000 INFO @ Thu, 09 Dec 2021 03:20:21: 6000000 INFO @ Thu, 09 Dec 2021 03:20:30: 4000000 INFO @ Thu, 09 Dec 2021 03:20:31: 9000000 INFO @ Thu, 09 Dec 2021 03:20:31: 7000000 INFO @ Thu, 09 Dec 2021 03:20:35: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:20:35: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:20:35: #1 total tags in treatment: 9394145 INFO @ Thu, 09 Dec 2021 03:20:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:20:35: #1 tags after filtering in treatment: 9394145 INFO @ Thu, 09 Dec 2021 03:20:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:20:35: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:20:36: #2 number of paired peaks: 306 WARNING @ Thu, 09 Dec 2021 03:20:36: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:36: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:36: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:36: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:36: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:36: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 03:20:36: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 03:20:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.05_model.r WARNING @ Thu, 09 Dec 2021 03:20:36: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:36: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 03:20:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:20:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:20:40: 5000000 INFO @ Thu, 09 Dec 2021 03:20:41: 8000000 INFO @ Thu, 09 Dec 2021 03:20:49: 6000000 INFO @ Thu, 09 Dec 2021 03:20:50: 9000000 INFO @ Thu, 09 Dec 2021 03:20:54: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:20:54: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:20:54: #1 total tags in treatment: 9394145 INFO @ Thu, 09 Dec 2021 03:20:54: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:20:54: #1 tags after filtering in treatment: 9394145 INFO @ Thu, 09 Dec 2021 03:20:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:20:54: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:54: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:54: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:20:55: #2 number of paired peaks: 306 WARNING @ Thu, 09 Dec 2021 03:20:55: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:55: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:55: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:55: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:55: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:55: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 03:20:55: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 03:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.10_model.r WARNING @ Thu, 09 Dec 2021 03:20:55: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:55: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 03:20:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:20:55: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:20:59: 7000000 INFO @ Thu, 09 Dec 2021 03:21:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:21:09: 8000000 INFO @ Thu, 09 Dec 2021 03:21:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:21:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:21:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.05_summits.bed INFO @ Thu, 09 Dec 2021 03:21:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (553 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:21:19: 9000000 INFO @ Thu, 09 Dec 2021 03:21:21: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:21:23: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:21:23: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:21:23: #1 total tags in treatment: 9394145 INFO @ Thu, 09 Dec 2021 03:21:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:21:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:21:23: #1 tags after filtering in treatment: 9394145 INFO @ Thu, 09 Dec 2021 03:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:21:23: #1 finished! INFO @ Thu, 09 Dec 2021 03:21:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:21:24: #2 number of paired peaks: 306 WARNING @ Thu, 09 Dec 2021 03:21:24: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Thu, 09 Dec 2021 03:21:24: start model_add_line... INFO @ Thu, 09 Dec 2021 03:21:24: start X-correlation... INFO @ Thu, 09 Dec 2021 03:21:24: end of X-cor INFO @ Thu, 09 Dec 2021 03:21:24: #2 finished! INFO @ Thu, 09 Dec 2021 03:21:24: #2 predicted fragment length is 52 bps INFO @ Thu, 09 Dec 2021 03:21:24: #2 alternative fragment length(s) may be 3,52 bps INFO @ Thu, 09 Dec 2021 03:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.20_model.r WARNING @ Thu, 09 Dec 2021 03:21:24: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:21:24: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Thu, 09 Dec 2021 03:21:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:21:24: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:21:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.10_summits.bed INFO @ Thu, 09 Dec 2021 03:21:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (350 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:21:50: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:22:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:22:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:22:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399008/SRX10399008.20_summits.bed INFO @ Thu, 09 Dec 2021 03:22:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 3 millis CompletedMACS2peakCalling