Job ID = 16432913 SRX = SRX13336904 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25074856 spots for SRR17152884/SRR17152884.sra Written 25074856 spots for SRR17152884/SRR17152884.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434867 ("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: 00:25:19 25074856 reads; of these: 25074856 (100.00%) were paired; of these: 20866641 (83.22%) aligned concordantly 0 times 3551067 (14.16%) aligned concordantly exactly 1 time 657148 (2.62%) aligned concordantly >1 times ---- 20866641 pairs aligned concordantly 0 times; of these: 2182369 (10.46%) aligned discordantly 1 time ---- 18684272 pairs aligned 0 times concordantly or discordantly; of these: 37368544 mates make up the pairs; of these: 36413026 (97.44%) aligned 0 times 500438 (1.34%) aligned exactly 1 time 455080 (1.22%) aligned >1 times 27.39% overall alignment rate Time searching: 00:25:19 Overall time: 00:25:19 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 661554 / 6374334 = 0.1038 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.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 @ Tue, 02 Aug 2022 10:11:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:11:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:11:45: 1000000 INFO @ Tue, 02 Aug 2022 10:11:57: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:12:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.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 @ Tue, 02 Aug 2022 10:12:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:12:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:12:10: 3000000 INFO @ Tue, 02 Aug 2022 10:12:17: 1000000 INFO @ Tue, 02 Aug 2022 10:12:22: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:12:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.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 @ Tue, 02 Aug 2022 10:12:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:12:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:12:33: 2000000 INFO @ Tue, 02 Aug 2022 10:12:35: 5000000 INFO @ Tue, 02 Aug 2022 10:12:47: 1000000 INFO @ Tue, 02 Aug 2022 10:12:47: 6000000 INFO @ Tue, 02 Aug 2022 10:12:48: 3000000 INFO @ Tue, 02 Aug 2022 10:13:00: 7000000 INFO @ Tue, 02 Aug 2022 10:13:02: 2000000 INFO @ Tue, 02 Aug 2022 10:13:04: 4000000 INFO @ Tue, 02 Aug 2022 10:13:12: 8000000 INFO @ Tue, 02 Aug 2022 10:13:17: 3000000 INFO @ Tue, 02 Aug 2022 10:13:19: 5000000 INFO @ Tue, 02 Aug 2022 10:13:25: 9000000 INFO @ Tue, 02 Aug 2022 10:13:32: 4000000 INFO @ Tue, 02 Aug 2022 10:13:34: 6000000 INFO @ Tue, 02 Aug 2022 10:13:38: 10000000 INFO @ Tue, 02 Aug 2022 10:13:47: 5000000 INFO @ Tue, 02 Aug 2022 10:13:48: 7000000 INFO @ Tue, 02 Aug 2022 10:13:54: 11000000 INFO @ Tue, 02 Aug 2022 10:14:00: 6000000 INFO @ Tue, 02 Aug 2022 10:14:02: 8000000 INFO @ Tue, 02 Aug 2022 10:14:08: 12000000 INFO @ Tue, 02 Aug 2022 10:14:14: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 10:14:14: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 10:14:14: #1 total tags in treatment: 3731022 INFO @ Tue, 02 Aug 2022 10:14:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:14:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:14:14: #1 tags after filtering in treatment: 3563067 INFO @ Tue, 02 Aug 2022 10:14:14: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 10:14:14: #1 finished! INFO @ Tue, 02 Aug 2022 10:14:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:14:14: #2 number of paired peaks: 547 WARNING @ Tue, 02 Aug 2022 10:14:14: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Tue, 02 Aug 2022 10:14:14: start model_add_line... INFO @ Tue, 02 Aug 2022 10:14:14: start X-correlation... INFO @ Tue, 02 Aug 2022 10:14:14: end of X-cor INFO @ Tue, 02 Aug 2022 10:14:14: #2 finished! INFO @ Tue, 02 Aug 2022 10:14:14: #2 predicted fragment length is 219 bps INFO @ Tue, 02 Aug 2022 10:14:14: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 02 Aug 2022 10:14:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.05_model.r WARNING @ Tue, 02 Aug 2022 10:14:14: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:14:14: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Tue, 02 Aug 2022 10:14:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:14:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:14:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:14:15: 7000000 INFO @ Tue, 02 Aug 2022 10:14:16: 9000000 INFO @ Tue, 02 Aug 2022 10:14:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:14:26: 8000000 INFO @ Tue, 02 Aug 2022 10:14:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:14:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:14:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.05_summits.bed INFO @ Tue, 02 Aug 2022 10:14:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:14:30: 10000000 INFO @ Tue, 02 Aug 2022 10:14:38: 9000000 INFO @ Tue, 02 Aug 2022 10:14:44: 11000000 INFO @ Tue, 02 Aug 2022 10:14:50: 10000000 INFO @ Tue, 02 Aug 2022 10:14:58: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:15:01: 11000000 INFO @ Tue, 02 Aug 2022 10:15:04: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 10:15:04: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 10:15:04: #1 total tags in treatment: 3731022 INFO @ Tue, 02 Aug 2022 10:15:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:15:04: #1 tags after filtering in treatment: 3563067 INFO @ Tue, 02 Aug 2022 10:15:04: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 10:15:04: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:04: #2 number of paired peaks: 547 WARNING @ Tue, 02 Aug 2022 10:15:04: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:04: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:04: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:04: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:04: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:04: #2 predicted fragment length is 219 bps INFO @ Tue, 02 Aug 2022 10:15:04: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 02 Aug 2022 10:15:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.10_model.r WARNING @ Tue, 02 Aug 2022 10:15:04: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:15:04: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Tue, 02 Aug 2022 10:15:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:15:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:15:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:15:13: 12000000 INFO @ Tue, 02 Aug 2022 10:15:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:15:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:15:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.10_summits.bed INFO @ Tue, 02 Aug 2022 10:15:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:15:18: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 10:15:18: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 10:15:18: #1 total tags in treatment: 3731022 INFO @ Tue, 02 Aug 2022 10:15:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:15:18: #1 tags after filtering in treatment: 3563067 INFO @ Tue, 02 Aug 2022 10:15:18: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 10:15:18: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:19: #2 number of paired peaks: 547 WARNING @ Tue, 02 Aug 2022 10:15:19: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:19: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:19: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:19: #2 predicted fragment length is 219 bps INFO @ Tue, 02 Aug 2022 10:15:19: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 02 Aug 2022 10:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.20_model.r WARNING @ Tue, 02 Aug 2022 10:15:19: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:15:19: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Tue, 02 Aug 2022 10:15:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:15:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:15:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336904/SRX13336904.20_summits.bed INFO @ Tue, 02 Aug 2022 10:15:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 34 millis CompletedMACS2peakCalling