Job ID = 14158098 SRX = SRX7739512 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15021344 spots for SRR11100916/SRR11100916.sra Written 15021344 spots for SRR11100916/SRR11100916.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158334 ("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: 00:03:35 15021344 reads; of these: 15021344 (100.00%) were unpaired; of these: 309502 (2.06%) aligned 0 times 12300121 (81.88%) aligned exactly 1 time 2411721 (16.06%) aligned >1 times 97.94% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 1466946 / 14711842 = 0.0997 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 14:28:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.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 14:28:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:28:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:28:49: 1000000 INFO @ Wed, 08 Dec 2021 14:28:54: 2000000 INFO @ Wed, 08 Dec 2021 14:28:59: 3000000 INFO @ Wed, 08 Dec 2021 14:29:04: 4000000 INFO @ Wed, 08 Dec 2021 14:29:09: 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 14:29:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.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 14:29:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:29:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:29:14: 6000000 INFO @ Wed, 08 Dec 2021 14:29:19: 1000000 INFO @ Wed, 08 Dec 2021 14:29:20: 7000000 INFO @ Wed, 08 Dec 2021 14:29:25: 2000000 INFO @ Wed, 08 Dec 2021 14:29:25: 8000000 INFO @ Wed, 08 Dec 2021 14:29:30: 3000000 INFO @ Wed, 08 Dec 2021 14:29:31: 9000000 INFO @ Wed, 08 Dec 2021 14:29:36: 4000000 INFO @ Wed, 08 Dec 2021 14:29:36: 10000000 INFO @ Wed, 08 Dec 2021 14:29:42: 5000000 INFO @ Wed, 08 Dec 2021 14:29:42: 11000000 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 14:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.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 14:29:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:29:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:29:47: 12000000 INFO @ Wed, 08 Dec 2021 14:29:47: 6000000 INFO @ Wed, 08 Dec 2021 14:29:51: 1000000 INFO @ Wed, 08 Dec 2021 14:29:52: 13000000 INFO @ Wed, 08 Dec 2021 14:29:53: 7000000 INFO @ Wed, 08 Dec 2021 14:29:54: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:29:54: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:29:54: #1 total tags in treatment: 13244896 INFO @ Wed, 08 Dec 2021 14:29:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:29:54: #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 14:29:54: #1 tags after filtering in treatment: 13244896 INFO @ Wed, 08 Dec 2021 14:29:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:29:54: #1 finished! INFO @ Wed, 08 Dec 2021 14:29:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:29:55: #2 number of paired peaks: 314 WARNING @ Wed, 08 Dec 2021 14:29:55: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Wed, 08 Dec 2021 14:29:55: start model_add_line... INFO @ Wed, 08 Dec 2021 14:29:55: start X-correlation... INFO @ Wed, 08 Dec 2021 14:29:55: end of X-cor INFO @ Wed, 08 Dec 2021 14:29:55: #2 finished! INFO @ Wed, 08 Dec 2021 14:29:55: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 14:29:55: #2 alternative fragment length(s) may be 3,52 bps INFO @ Wed, 08 Dec 2021 14:29:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.05_model.r WARNING @ Wed, 08 Dec 2021 14:29:55: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:29:55: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Wed, 08 Dec 2021 14:29:55: #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 14:29:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:29:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:29:58: 2000000 INFO @ Wed, 08 Dec 2021 14:29:58: 8000000 INFO @ Wed, 08 Dec 2021 14:30:04: 9000000 INFO @ Wed, 08 Dec 2021 14:30:05: 3000000 INFO @ Wed, 08 Dec 2021 14:30:10: 10000000 INFO @ Wed, 08 Dec 2021 14:30:12: 4000000 INFO @ Wed, 08 Dec 2021 14:30:15: 11000000 INFO @ Wed, 08 Dec 2021 14:30:19: 5000000 INFO @ Wed, 08 Dec 2021 14:30:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:30:21: 12000000 INFO @ Wed, 08 Dec 2021 14:30:26: 6000000 INFO @ Wed, 08 Dec 2021 14:30:26: 13000000 INFO @ Wed, 08 Dec 2021 14:30:27: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:30:27: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:30:27: #1 total tags in treatment: 13244896 INFO @ Wed, 08 Dec 2021 14:30:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:30:27: #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 14:30:28: #1 tags after filtering in treatment: 13244896 INFO @ Wed, 08 Dec 2021 14:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:30:28: #1 finished! INFO @ Wed, 08 Dec 2021 14:30:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:30:29: #2 number of paired peaks: 314 WARNING @ Wed, 08 Dec 2021 14:30:29: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Wed, 08 Dec 2021 14:30:29: start model_add_line... INFO @ Wed, 08 Dec 2021 14:30:29: start X-correlation... INFO @ Wed, 08 Dec 2021 14:30:29: end of X-cor INFO @ Wed, 08 Dec 2021 14:30:29: #2 finished! INFO @ Wed, 08 Dec 2021 14:30:29: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 14:30:29: #2 alternative fragment length(s) may be 3,52 bps INFO @ Wed, 08 Dec 2021 14:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.10_model.r WARNING @ Wed, 08 Dec 2021 14:30:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:30:29: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Wed, 08 Dec 2021 14:30:29: #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 14:30:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:30:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:30:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:30:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.05_summits.bed INFO @ Wed, 08 Dec 2021 14:30:31: Done! pass1 - making usageList (7 chroms): 0 millis INFO @ Wed, 08 Dec 2021 14:30:33: 7000000 pass2 - checking and writing primary data (907 records, 4 fields): 1264 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:30:39: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:30:46: 9000000 INFO @ Wed, 08 Dec 2021 14:30:53: 10000000 INFO @ Wed, 08 Dec 2021 14:30:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:30:59: 11000000 INFO @ Wed, 08 Dec 2021 14:31:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:31:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.10_summits.bed INFO @ Wed, 08 Dec 2021 14:31:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (531 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:31:06: 12000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:31:12: 13000000 INFO @ Wed, 08 Dec 2021 14:31:14: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:31:14: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:31:14: #1 total tags in treatment: 13244896 INFO @ Wed, 08 Dec 2021 14:31:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:14: #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 14:31:14: #1 tags after filtering in treatment: 13244896 INFO @ Wed, 08 Dec 2021 14:31:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:31:14: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:15: #2 number of paired peaks: 314 WARNING @ Wed, 08 Dec 2021 14:31:15: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:15: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:15: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:15: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:15: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:15: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 14:31:15: #2 alternative fragment length(s) may be 3,52 bps INFO @ Wed, 08 Dec 2021 14:31:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.20_model.r WARNING @ Wed, 08 Dec 2021 14:31:15: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:31:15: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Wed, 08 Dec 2021 14:31:15: #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 14:31:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:31:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7739512/SRX7739512.20_summits.bed INFO @ Wed, 08 Dec 2021 14:31:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (238 records, 4 fields): 2 millis CompletedMACS2peakCalling