Job ID = 12264808 SRX = SRX7246265 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5345504 spots for SRR10564677/SRR10564677.sra Written 5345504 spots for SRR10564677/SRR10564677.sra Read 5387100 spots for SRR10564678/SRR10564678.sra Written 5387100 spots for SRR10564678/SRR10564678.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265333 ("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: 00:20:06 10732604 reads; of these: 10732604 (100.00%) were paired; of these: 658865 (6.14%) aligned concordantly 0 times 8135629 (75.80%) aligned concordantly exactly 1 time 1938110 (18.06%) aligned concordantly >1 times ---- 658865 pairs aligned concordantly 0 times; of these: 191168 (29.01%) aligned discordantly 1 time ---- 467697 pairs aligned 0 times concordantly or discordantly; of these: 935394 mates make up the pairs; of these: 710361 (75.94%) aligned 0 times 123580 (13.21%) aligned exactly 1 time 101453 (10.85%) aligned >1 times 96.69% overall alignment rate Time searching: 00:20:06 Overall time: 00:20:06 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] 2228290 / 7171550 = 0.3107 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.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 @ Sat, 03 Apr 2021 06:26:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:26:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:27:04: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:27:18: 2000000 INFO @ Sat, 03 Apr 2021 06:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.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 @ Sat, 03 Apr 2021 06:27:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:27:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:27:32: 3000000 INFO @ Sat, 03 Apr 2021 06:27:34: 1000000 INFO @ Sat, 03 Apr 2021 06:27:47: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:27:48: 2000000 INFO @ Sat, 03 Apr 2021 06:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.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 @ Sat, 03 Apr 2021 06:27:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:27:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:28:02: 3000000 INFO @ Sat, 03 Apr 2021 06:28:03: 5000000 INFO @ Sat, 03 Apr 2021 06:28:06: 1000000 INFO @ Sat, 03 Apr 2021 06:28:16: 4000000 INFO @ Sat, 03 Apr 2021 06:28:19: 6000000 INFO @ Sat, 03 Apr 2021 06:28:20: 2000000 INFO @ Sat, 03 Apr 2021 06:28:29: 5000000 INFO @ Sat, 03 Apr 2021 06:28:33: 3000000 INFO @ Sat, 03 Apr 2021 06:28:35: 7000000 INFO @ Sat, 03 Apr 2021 06:28:43: 6000000 INFO @ Sat, 03 Apr 2021 06:28:46: 4000000 INFO @ Sat, 03 Apr 2021 06:28:51: 8000000 INFO @ Sat, 03 Apr 2021 06:28:58: 7000000 INFO @ Sat, 03 Apr 2021 06:29:00: 5000000 INFO @ Sat, 03 Apr 2021 06:29:06: 9000000 INFO @ Sat, 03 Apr 2021 06:29:13: 8000000 INFO @ Sat, 03 Apr 2021 06:29:15: 6000000 INFO @ Sat, 03 Apr 2021 06:29:24: 10000000 INFO @ Sat, 03 Apr 2021 06:29:27: 9000000 INFO @ Sat, 03 Apr 2021 06:29:29: 7000000 INFO @ Sat, 03 Apr 2021 06:29:39: 11000000 INFO @ Sat, 03 Apr 2021 06:29:42: 10000000 INFO @ Sat, 03 Apr 2021 06:29:42: 8000000 INFO @ Sat, 03 Apr 2021 06:29:54: 12000000 INFO @ Sat, 03 Apr 2021 06:29:54: 11000000 INFO @ Sat, 03 Apr 2021 06:29:54: 9000000 INFO @ Sat, 03 Apr 2021 06:30:07: 10000000 INFO @ Sat, 03 Apr 2021 06:30:07: 12000000 INFO @ Sat, 03 Apr 2021 06:30:09: 13000000 INFO @ Sat, 03 Apr 2021 06:30:20: 11000000 INFO @ Sat, 03 Apr 2021 06:30:21: 13000000 INFO @ Sat, 03 Apr 2021 06:30:24: 14000000 INFO @ Sat, 03 Apr 2021 06:30:32: 14000000 INFO @ Sat, 03 Apr 2021 06:30:33: 12000000 INFO @ Sat, 03 Apr 2021 06:30:37: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:30:43: 15000000 INFO @ Sat, 03 Apr 2021 06:30:45: 13000000 INFO @ Sat, 03 Apr 2021 06:30:50: 16000000 INFO @ Sat, 03 Apr 2021 06:30:54: #1 tag size is determined as 91 bps INFO @ Sat, 03 Apr 2021 06:30:54: #1 tag size = 91 INFO @ Sat, 03 Apr 2021 06:30:54: #1 total tags in treatment: 7851763 INFO @ Sat, 03 Apr 2021 06:30:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:30:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:30:54: 16000000 INFO @ Sat, 03 Apr 2021 06:30:54: #1 tags after filtering in treatment: 5485635 INFO @ Sat, 03 Apr 2021 06:30:54: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:30:54: #1 finished! INFO @ Sat, 03 Apr 2021 06:30:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:30:55: #2 number of paired peaks: 621 WARNING @ Sat, 03 Apr 2021 06:30:55: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Sat, 03 Apr 2021 06:30:55: start model_add_line... INFO @ Sat, 03 Apr 2021 06:30:55: start X-correlation... INFO @ Sat, 03 Apr 2021 06:30:55: end of X-cor INFO @ Sat, 03 Apr 2021 06:30:55: #2 finished! INFO @ Sat, 03 Apr 2021 06:30:55: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Apr 2021 06:30:55: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Apr 2021 06:30:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.05_model.r WARNING @ Sat, 03 Apr 2021 06:30:55: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:30:55: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 03 Apr 2021 06:30:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:30:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:30:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:30:55: 14000000 INFO @ Sat, 03 Apr 2021 06:30:57: #1 tag size is determined as 91 bps INFO @ Sat, 03 Apr 2021 06:30:57: #1 tag size = 91 INFO @ Sat, 03 Apr 2021 06:30:57: #1 total tags in treatment: 7851763 INFO @ Sat, 03 Apr 2021 06:30:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:30:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:30:58: #1 tags after filtering in treatment: 5485635 INFO @ Sat, 03 Apr 2021 06:30:58: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:30:58: #1 finished! INFO @ Sat, 03 Apr 2021 06:30:58: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:30:58: #2 number of paired peaks: 621 WARNING @ Sat, 03 Apr 2021 06:30:58: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Sat, 03 Apr 2021 06:30:58: start model_add_line... INFO @ Sat, 03 Apr 2021 06:30:58: start X-correlation... INFO @ Sat, 03 Apr 2021 06:30:58: end of X-cor INFO @ Sat, 03 Apr 2021 06:30:58: #2 finished! INFO @ Sat, 03 Apr 2021 06:30:58: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Apr 2021 06:30:58: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Apr 2021 06:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.10_model.r WARNING @ Sat, 03 Apr 2021 06:30:58: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:30:58: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 03 Apr 2021 06:30:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:30:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:31:06: 15000000 INFO @ Sat, 03 Apr 2021 06:31:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:31:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.05_summits.bed INFO @ Sat, 03 Apr 2021 06:31:16: Done! pass1 - making usageList (7 chroms): 14 millis pass2 - checking and writing primary data (2929 records, 4 fields): 23 millis INFO @ Sat, 03 Apr 2021 06:31:16: 16000000 CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:31:19: #1 tag size is determined as 91 bps INFO @ Sat, 03 Apr 2021 06:31:19: #1 tag size = 91 INFO @ Sat, 03 Apr 2021 06:31:19: #1 total tags in treatment: 7851763 INFO @ Sat, 03 Apr 2021 06:31:19: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:31:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:31:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:31:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:31:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.10_summits.bed INFO @ Sat, 03 Apr 2021 06:31:19: Done! INFO @ Sat, 03 Apr 2021 06:31:19: #1 tags after filtering in treatment: 5485635 INFO @ Sat, 03 Apr 2021 06:31:19: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:31:19: #1 finished! INFO @ Sat, 03 Apr 2021 06:31:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:31:19: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1630 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:31:19: #2 number of paired peaks: 621 WARNING @ Sat, 03 Apr 2021 06:31:19: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Sat, 03 Apr 2021 06:31:19: start model_add_line... INFO @ Sat, 03 Apr 2021 06:31:19: start X-correlation... INFO @ Sat, 03 Apr 2021 06:31:19: end of X-cor INFO @ Sat, 03 Apr 2021 06:31:19: #2 finished! INFO @ Sat, 03 Apr 2021 06:31:19: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Apr 2021 06:31:19: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Apr 2021 06:31:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.20_model.r WARNING @ Sat, 03 Apr 2021 06:31:19: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:31:19: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 03 Apr 2021 06:31:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:31:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:31:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:31:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:31:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:31:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:31:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246265/SRX7246265.20_summits.bed INFO @ Sat, 03 Apr 2021 06:31:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling