Job ID = 12264747 SRX = SRX2333000 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21258521 spots for SRR5000680/SRR5000680.sra Written 21258521 spots for SRR5000680/SRR5000680.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265145 ("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: 00:09:17 21258521 reads; of these: 21258521 (100.00%) were paired; of these: 19296529 (90.77%) aligned concordantly 0 times 1640569 (7.72%) aligned concordantly exactly 1 time 321423 (1.51%) aligned concordantly >1 times ---- 19296529 pairs aligned concordantly 0 times; of these: 423667 (2.20%) aligned discordantly 1 time ---- 18872862 pairs aligned 0 times concordantly or discordantly; of these: 37745724 mates make up the pairs; of these: 37547866 (99.48%) aligned 0 times 71504 (0.19%) aligned exactly 1 time 126354 (0.33%) aligned >1 times 11.69% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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_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] 975698 / 2365654 = 0.4124 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 06:06:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.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 06:06:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:15: 1000000 INFO @ Sat, 03 Apr 2021 06:06:23: 2000000 INFO @ Sat, 03 Apr 2021 06:06:32: 3000000 INFO @ Sat, 03 Apr 2021 06:06:32: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:06:32: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:06:32: #1 total tags in treatment: 1183338 INFO @ Sat, 03 Apr 2021 06:06:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:06:32: #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 06:06:32: #1 tags after filtering in treatment: 902814 INFO @ Sat, 03 Apr 2021 06:06:32: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 06:06:32: #1 finished! INFO @ Sat, 03 Apr 2021 06:06:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:06:32: #2 number of paired peaks: 666 WARNING @ Sat, 03 Apr 2021 06:06:32: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Sat, 03 Apr 2021 06:06:32: start model_add_line... INFO @ Sat, 03 Apr 2021 06:06:32: start X-correlation... INFO @ Sat, 03 Apr 2021 06:06:32: end of X-cor INFO @ Sat, 03 Apr 2021 06:06:32: #2 finished! INFO @ Sat, 03 Apr 2021 06:06:32: #2 predicted fragment length is 172 bps INFO @ Sat, 03 Apr 2021 06:06:32: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 03 Apr 2021 06:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.05_model.r WARNING @ Sat, 03 Apr 2021 06:06:32: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:06:32: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 03 Apr 2021 06:06:32: #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 06:06:32: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:06:32: #3 Pre-compute pvalue-qvalue table... 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 06:06:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:06:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.05_summits.bed INFO @ Sat, 03 Apr 2021 06:06:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (344 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:06:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.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 06:06:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:45: 1000000 INFO @ Sat, 03 Apr 2021 06:06:54: 2000000 INFO @ Sat, 03 Apr 2021 06:07:03: 3000000 INFO @ Sat, 03 Apr 2021 06:07:03: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:07:03: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:07:03: #1 total tags in treatment: 1183338 INFO @ Sat, 03 Apr 2021 06:07:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:07:03: #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 06:07:03: #1 tags after filtering in treatment: 902814 INFO @ Sat, 03 Apr 2021 06:07:03: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 06:07:03: #1 finished! INFO @ Sat, 03 Apr 2021 06:07:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:03: #2 number of paired peaks: 666 WARNING @ Sat, 03 Apr 2021 06:07:03: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Sat, 03 Apr 2021 06:07:03: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:03: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:03: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:03: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:03: #2 predicted fragment length is 172 bps INFO @ Sat, 03 Apr 2021 06:07:03: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 03 Apr 2021 06:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.10_model.r WARNING @ Sat, 03 Apr 2021 06:07:03: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:03: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 03 Apr 2021 06:07:03: #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 06:07:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:03: #3 Pre-compute pvalue-qvalue table... 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 06:07:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:07:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:07:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.10_summits.bed INFO @ Sat, 03 Apr 2021 06:07:06: Done! INFO @ Sat, 03 Apr 2021 06:07:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.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 06:07:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:06: #1 read treatment tags... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:07:15: 1000000 INFO @ Sat, 03 Apr 2021 06:07:23: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:07:31: 3000000 INFO @ Sat, 03 Apr 2021 06:07:31: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:07:31: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:07:31: #1 total tags in treatment: 1183338 INFO @ Sat, 03 Apr 2021 06:07:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:07:31: #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 06:07:31: #1 tags after filtering in treatment: 902814 INFO @ Sat, 03 Apr 2021 06:07:31: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 06:07:31: #1 finished! INFO @ Sat, 03 Apr 2021 06:07:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:31: #2 number of paired peaks: 666 WARNING @ Sat, 03 Apr 2021 06:07:31: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Sat, 03 Apr 2021 06:07:31: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:31: #2 predicted fragment length is 172 bps INFO @ Sat, 03 Apr 2021 06:07:31: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 03 Apr 2021 06:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.20_model.r WARNING @ Sat, 03 Apr 2021 06:07:31: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:31: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 03 Apr 2021 06:07:31: #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 06:07:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:07:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:07:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:07:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:07:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333000/SRX2333000.20_summits.bed INFO @ Sat, 03 Apr 2021 06:07:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 2 millis CompletedMACS2peakCalling