Job ID = 14160348 SRX = SRX9567172 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21858738 spots for SRR13125147/SRR13125147.sra Written 21858738 spots for SRR13125147/SRR13125147.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160633 ("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: 01:17:50 21858738 reads; of these: 21858738 (100.00%) were paired; of these: 7098473 (32.47%) aligned concordantly 0 times 6278767 (28.72%) aligned concordantly exactly 1 time 8481498 (38.80%) aligned concordantly >1 times ---- 7098473 pairs aligned concordantly 0 times; of these: 4095676 (57.70%) aligned discordantly 1 time ---- 3002797 pairs aligned 0 times concordantly or discordantly; of these: 6005594 mates make up the pairs; of these: 3673532 (61.17%) aligned 0 times 987879 (16.45%) aligned exactly 1 time 1344183 (22.38%) aligned >1 times 91.60% overall alignment rate Time searching: 01:17:50 Overall time: 01:17:50 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] 14938121 / 18821014 = 0.7937 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 03:07:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.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 03:07:25: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:25: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:32: 1000000 INFO @ Thu, 09 Dec 2021 03:07:39: 2000000 INFO @ Thu, 09 Dec 2021 03:07:47: 3000000 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 03:07:54: 4000000 INFO @ Thu, 09 Dec 2021 03:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.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 03:07:55: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:55: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:08:02: 5000000 INFO @ Thu, 09 Dec 2021 03:08:03: 1000000 INFO @ Thu, 09 Dec 2021 03:08:10: 6000000 INFO @ Thu, 09 Dec 2021 03:08:12: 2000000 INFO @ Thu, 09 Dec 2021 03:08:19: 7000000 INFO @ Thu, 09 Dec 2021 03:08:20: 3000000 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 03:08:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.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 03:08:25: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:08:25: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:08:27: 8000000 INFO @ Thu, 09 Dec 2021 03:08:29: 4000000 INFO @ Thu, 09 Dec 2021 03:08:36: 1000000 INFO @ Thu, 09 Dec 2021 03:08:37: 9000000 INFO @ Thu, 09 Dec 2021 03:08:39: 5000000 INFO @ Thu, 09 Dec 2021 03:08:46: 10000000 INFO @ Thu, 09 Dec 2021 03:08:47: 2000000 INFO @ Thu, 09 Dec 2021 03:08:48: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:08:48: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:08:48: #1 total tags in treatment: 3019138 INFO @ Thu, 09 Dec 2021 03:08:48: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:08:48: #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 03:08:48: #1 tags after filtering in treatment: 1673683 INFO @ Thu, 09 Dec 2021 03:08:48: #1 Redundant rate of treatment: 0.45 INFO @ Thu, 09 Dec 2021 03:08:48: #1 finished! INFO @ Thu, 09 Dec 2021 03:08:48: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:08:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:08:48: #2 number of paired peaks: 989 WARNING @ Thu, 09 Dec 2021 03:08:48: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Thu, 09 Dec 2021 03:08:48: start model_add_line... INFO @ Thu, 09 Dec 2021 03:08:48: start X-correlation... INFO @ Thu, 09 Dec 2021 03:08:48: end of X-cor INFO @ Thu, 09 Dec 2021 03:08:48: #2 finished! INFO @ Thu, 09 Dec 2021 03:08:48: #2 predicted fragment length is 297 bps INFO @ Thu, 09 Dec 2021 03:08:48: #2 alternative fragment length(s) may be 297 bps INFO @ Thu, 09 Dec 2021 03:08:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.05_model.r WARNING @ Thu, 09 Dec 2021 03:08:48: #2 Since the d (297) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:08:48: #2 You may need to consider one of the other alternative d(s): 297 WARNING @ Thu, 09 Dec 2021 03:08:48: #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 03:08:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:08:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:08:48: 6000000 INFO @ Thu, 09 Dec 2021 03:08:53: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:08:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:08:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:08:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.05_summits.bed INFO @ Thu, 09 Dec 2021 03:08:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (709 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:08:57: 3000000 INFO @ Thu, 09 Dec 2021 03:08:57: 7000000 INFO @ Thu, 09 Dec 2021 03:09:06: 8000000 INFO @ Thu, 09 Dec 2021 03:09:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:09:15: 9000000 INFO @ Thu, 09 Dec 2021 03:09:17: 5000000 INFO @ Thu, 09 Dec 2021 03:09:24: 10000000 INFO @ Thu, 09 Dec 2021 03:09:26: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:09:26: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:09:26: #1 total tags in treatment: 3019138 INFO @ Thu, 09 Dec 2021 03:09:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:09:26: #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 03:09:26: #1 tags after filtering in treatment: 1673683 INFO @ Thu, 09 Dec 2021 03:09:26: #1 Redundant rate of treatment: 0.45 INFO @ Thu, 09 Dec 2021 03:09:26: #1 finished! INFO @ Thu, 09 Dec 2021 03:09:26: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:09:26: #2 number of paired peaks: 989 WARNING @ Thu, 09 Dec 2021 03:09:26: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Thu, 09 Dec 2021 03:09:26: start model_add_line... INFO @ Thu, 09 Dec 2021 03:09:26: start X-correlation... INFO @ Thu, 09 Dec 2021 03:09:26: end of X-cor INFO @ Thu, 09 Dec 2021 03:09:26: #2 finished! INFO @ Thu, 09 Dec 2021 03:09:26: #2 predicted fragment length is 297 bps INFO @ Thu, 09 Dec 2021 03:09:26: #2 alternative fragment length(s) may be 297 bps INFO @ Thu, 09 Dec 2021 03:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.10_model.r WARNING @ Thu, 09 Dec 2021 03:09:26: #2 Since the d (297) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:09:26: #2 You may need to consider one of the other alternative d(s): 297 WARNING @ Thu, 09 Dec 2021 03:09:26: #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 03:09:26: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:09:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:09:27: 6000000 INFO @ Thu, 09 Dec 2021 03:09:31: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.10_summits.bed INFO @ Thu, 09 Dec 2021 03:09:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:09:37: 7000000 INFO @ Thu, 09 Dec 2021 03:09:46: 8000000 INFO @ Thu, 09 Dec 2021 03:09:56: 9000000 INFO @ Thu, 09 Dec 2021 03:10:05: 10000000 INFO @ Thu, 09 Dec 2021 03:10:06: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:10:06: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:10:06: #1 total tags in treatment: 3019138 INFO @ Thu, 09 Dec 2021 03:10:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:10:06: #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 03:10:06: #1 tags after filtering in treatment: 1673683 INFO @ Thu, 09 Dec 2021 03:10:06: #1 Redundant rate of treatment: 0.45 INFO @ Thu, 09 Dec 2021 03:10:06: #1 finished! INFO @ Thu, 09 Dec 2021 03:10:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:10:06: #2 number of paired peaks: 989 WARNING @ Thu, 09 Dec 2021 03:10:06: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Thu, 09 Dec 2021 03:10:06: start model_add_line... INFO @ Thu, 09 Dec 2021 03:10:06: start X-correlation... INFO @ Thu, 09 Dec 2021 03:10:06: end of X-cor INFO @ Thu, 09 Dec 2021 03:10:06: #2 finished! INFO @ Thu, 09 Dec 2021 03:10:06: #2 predicted fragment length is 297 bps INFO @ Thu, 09 Dec 2021 03:10:06: #2 alternative fragment length(s) may be 297 bps INFO @ Thu, 09 Dec 2021 03:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.20_model.r WARNING @ Thu, 09 Dec 2021 03:10:07: #2 Since the d (297) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:10:07: #2 You may need to consider one of the other alternative d(s): 297 WARNING @ Thu, 09 Dec 2021 03:10:07: #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 03:10:07: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:10:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:10:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567172/SRX9567172.20_summits.bed INFO @ Thu, 09 Dec 2021 03:10:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (434 records, 4 fields): 2 millis CompletedMACS2peakCalling