Job ID = 14160367 SRX = SRX9567184 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22945901 spots for SRR13125159/SRR13125159.sra Written 22945901 spots for SRR13125159/SRR13125159.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160617 ("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: 01:00:09 22945901 reads; of these: 22945901 (100.00%) were paired; of these: 8376705 (36.51%) aligned concordantly 0 times 12548682 (54.69%) aligned concordantly exactly 1 time 2020514 (8.81%) aligned concordantly >1 times ---- 8376705 pairs aligned concordantly 0 times; of these: 5819383 (69.47%) aligned discordantly 1 time ---- 2557322 pairs aligned 0 times concordantly or discordantly; of these: 5114644 mates make up the pairs; of these: 2453432 (47.97%) aligned 0 times 1326792 (25.94%) aligned exactly 1 time 1334420 (26.09%) aligned >1 times 94.65% overall alignment rate Time searching: 01:00:10 Overall time: 01:00:10 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 32 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] 13787569 / 20364649 = 0.6770 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 03:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.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 03:09:49: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:09:49: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:09:58: 1000000 INFO @ Thu, 09 Dec 2021 03:10:08: 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 03:10:17: 3000000 INFO @ Thu, 09 Dec 2021 03:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.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 03:10:18: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:10:18: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:10:27: 4000000 INFO @ Thu, 09 Dec 2021 03:10:27: 1000000 INFO @ Thu, 09 Dec 2021 03:10:36: 5000000 INFO @ Thu, 09 Dec 2021 03:10:38: 2000000 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 03:10:46: 6000000 INFO @ Thu, 09 Dec 2021 03:10:47: 3000000 INFO @ Thu, 09 Dec 2021 03:10:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.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 03:10:48: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:10:48: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:10:55: 7000000 INFO @ Thu, 09 Dec 2021 03:10:56: 4000000 INFO @ Thu, 09 Dec 2021 03:10:58: 1000000 INFO @ Thu, 09 Dec 2021 03:11:06: 8000000 INFO @ Thu, 09 Dec 2021 03:11:06: 5000000 INFO @ Thu, 09 Dec 2021 03:11:09: 2000000 INFO @ Thu, 09 Dec 2021 03:11:16: 9000000 INFO @ Thu, 09 Dec 2021 03:11:17: 6000000 INFO @ Thu, 09 Dec 2021 03:11:19: 3000000 INFO @ Thu, 09 Dec 2021 03:11:25: 10000000 INFO @ Thu, 09 Dec 2021 03:11:27: 7000000 INFO @ Thu, 09 Dec 2021 03:11:30: 4000000 INFO @ Thu, 09 Dec 2021 03:11:35: 11000000 INFO @ Thu, 09 Dec 2021 03:11:38: 8000000 INFO @ Thu, 09 Dec 2021 03:11:41: 5000000 INFO @ Thu, 09 Dec 2021 03:11:45: 12000000 INFO @ Thu, 09 Dec 2021 03:11:49: 9000000 INFO @ Thu, 09 Dec 2021 03:11:52: 6000000 INFO @ Thu, 09 Dec 2021 03:11:55: 13000000 INFO @ Thu, 09 Dec 2021 03:11:59: 10000000 INFO @ Thu, 09 Dec 2021 03:12:03: 7000000 INFO @ Thu, 09 Dec 2021 03:12:05: 14000000 INFO @ Thu, 09 Dec 2021 03:12:10: 11000000 INFO @ Thu, 09 Dec 2021 03:12:14: 8000000 INFO @ Thu, 09 Dec 2021 03:12:14: 15000000 INFO @ Thu, 09 Dec 2021 03:12:20: 12000000 INFO @ Thu, 09 Dec 2021 03:12:23: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:12:23: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:12:23: #1 total tags in treatment: 4805731 INFO @ Thu, 09 Dec 2021 03:12:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:12:23: #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 03:12:23: #1 tags after filtering in treatment: 4316564 INFO @ Thu, 09 Dec 2021 03:12:23: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:12:23: #1 finished! INFO @ Thu, 09 Dec 2021 03:12:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:12:24: #2 number of paired peaks: 676 WARNING @ Thu, 09 Dec 2021 03:12:24: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Thu, 09 Dec 2021 03:12:24: start model_add_line... INFO @ Thu, 09 Dec 2021 03:12:24: start X-correlation... INFO @ Thu, 09 Dec 2021 03:12:24: end of X-cor INFO @ Thu, 09 Dec 2021 03:12:24: #2 finished! INFO @ Thu, 09 Dec 2021 03:12:24: #2 predicted fragment length is 229 bps INFO @ Thu, 09 Dec 2021 03:12:24: #2 alternative fragment length(s) may be 229 bps INFO @ Thu, 09 Dec 2021 03:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.05_model.r WARNING @ Thu, 09 Dec 2021 03:12:24: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:12:24: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Thu, 09 Dec 2021 03:12:24: #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 03:12:24: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:12:25: 9000000 INFO @ Thu, 09 Dec 2021 03:12:31: 13000000 INFO @ Thu, 09 Dec 2021 03:12:35: 10000000 INFO @ Thu, 09 Dec 2021 03:12:39: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:12:41: 14000000 INFO @ Thu, 09 Dec 2021 03:12:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:12:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:12:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.05_summits.bed INFO @ Thu, 09 Dec 2021 03:12:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:12:45: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:12:52: 15000000 INFO @ Thu, 09 Dec 2021 03:12:56: 12000000 INFO @ Thu, 09 Dec 2021 03:13:01: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:13:01: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:13:01: #1 total tags in treatment: 4805731 INFO @ Thu, 09 Dec 2021 03:13:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:13:01: #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 03:13:01: #1 tags after filtering in treatment: 4316564 INFO @ Thu, 09 Dec 2021 03:13:01: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:13:01: #1 finished! INFO @ Thu, 09 Dec 2021 03:13:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:13:02: #2 number of paired peaks: 676 WARNING @ Thu, 09 Dec 2021 03:13:02: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Thu, 09 Dec 2021 03:13:02: start model_add_line... INFO @ Thu, 09 Dec 2021 03:13:02: start X-correlation... INFO @ Thu, 09 Dec 2021 03:13:02: end of X-cor INFO @ Thu, 09 Dec 2021 03:13:02: #2 finished! INFO @ Thu, 09 Dec 2021 03:13:02: #2 predicted fragment length is 229 bps INFO @ Thu, 09 Dec 2021 03:13:02: #2 alternative fragment length(s) may be 229 bps INFO @ Thu, 09 Dec 2021 03:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.10_model.r WARNING @ Thu, 09 Dec 2021 03:13:02: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:13:02: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Thu, 09 Dec 2021 03:13:02: #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 03:13:02: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:13:05: 13000000 INFO @ Thu, 09 Dec 2021 03:13:15: 14000000 INFO @ Thu, 09 Dec 2021 03:13:17: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:13:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.10_summits.bed INFO @ Thu, 09 Dec 2021 03:13:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (384 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:13:25: 15000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:13:33: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:13:33: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:13:33: #1 total tags in treatment: 4805731 INFO @ Thu, 09 Dec 2021 03:13:33: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:13:33: #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 03:13:33: #1 tags after filtering in treatment: 4316564 INFO @ Thu, 09 Dec 2021 03:13:33: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:13:33: #1 finished! INFO @ Thu, 09 Dec 2021 03:13:33: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:13:34: #2 number of paired peaks: 676 WARNING @ Thu, 09 Dec 2021 03:13:34: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Thu, 09 Dec 2021 03:13:34: start model_add_line... INFO @ Thu, 09 Dec 2021 03:13:34: start X-correlation... INFO @ Thu, 09 Dec 2021 03:13:34: end of X-cor INFO @ Thu, 09 Dec 2021 03:13:34: #2 finished! INFO @ Thu, 09 Dec 2021 03:13:34: #2 predicted fragment length is 229 bps INFO @ Thu, 09 Dec 2021 03:13:34: #2 alternative fragment length(s) may be 229 bps INFO @ Thu, 09 Dec 2021 03:13:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.20_model.r WARNING @ Thu, 09 Dec 2021 03:13:34: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:13:34: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Thu, 09 Dec 2021 03:13:34: #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 03:13:34: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:13:49: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:13:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:13:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:13:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567184/SRX9567184.20_summits.bed INFO @ Thu, 09 Dec 2021 03:13:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 28 millis CompletedMACS2peakCalling