Job ID = 14160373 SRX = SRX9567189 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27990264 spots for SRR13125164/SRR13125164.sra Written 27990264 spots for SRR13125164/SRR13125164.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160625 ("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: 00:56:14 27990264 reads; of these: 27990264 (100.00%) were paired; of these: 8836347 (31.57%) aligned concordantly 0 times 16586136 (59.26%) aligned concordantly exactly 1 time 2567781 (9.17%) aligned concordantly >1 times ---- 8836347 pairs aligned concordantly 0 times; of these: 5167733 (58.48%) aligned discordantly 1 time ---- 3668614 pairs aligned 0 times concordantly or discordantly; of these: 7337228 mates make up the pairs; of these: 4835855 (65.91%) aligned 0 times 1279055 (17.43%) aligned exactly 1 time 1222318 (16.66%) aligned >1 times 91.36% overall alignment rate Time searching: 00:56:14 Overall time: 00:56:14 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 40 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] 18812073 / 24288183 = 0.7745 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 03:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.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 03:06:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:06:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:06:50: 1000000 INFO @ Thu, 09 Dec 2021 03:06:58: 2000000 INFO @ Thu, 09 Dec 2021 03:07:05: 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 03:07:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.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 03:07:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:13: 4000000 INFO @ Thu, 09 Dec 2021 03:07:21: 1000000 INFO @ Thu, 09 Dec 2021 03:07:21: 5000000 INFO @ Thu, 09 Dec 2021 03:07:29: 2000000 INFO @ Thu, 09 Dec 2021 03:07:29: 6000000 INFO @ Thu, 09 Dec 2021 03:07:37: 3000000 INFO @ Thu, 09 Dec 2021 03:07:37: 7000000 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 03:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.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 03:07:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:45: 4000000 INFO @ Thu, 09 Dec 2021 03:07:45: 8000000 INFO @ Thu, 09 Dec 2021 03:07:52: 1000000 INFO @ Thu, 09 Dec 2021 03:07:54: 5000000 INFO @ Thu, 09 Dec 2021 03:07:54: 9000000 INFO @ Thu, 09 Dec 2021 03:08:01: 2000000 INFO @ Thu, 09 Dec 2021 03:08:03: 6000000 INFO @ Thu, 09 Dec 2021 03:08:04: 10000000 INFO @ Thu, 09 Dec 2021 03:08:10: 3000000 INFO @ Thu, 09 Dec 2021 03:08:13: 7000000 INFO @ Thu, 09 Dec 2021 03:08:13: 11000000 INFO @ Thu, 09 Dec 2021 03:08:19: 4000000 INFO @ Thu, 09 Dec 2021 03:08:22: 8000000 INFO @ Thu, 09 Dec 2021 03:08:22: 12000000 INFO @ Thu, 09 Dec 2021 03:08:28: 5000000 INFO @ Thu, 09 Dec 2021 03:08:31: 9000000 INFO @ Thu, 09 Dec 2021 03:08:31: 13000000 INFO @ Thu, 09 Dec 2021 03:08:36: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:08:36: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:08:36: #1 total tags in treatment: 4350615 INFO @ Thu, 09 Dec 2021 03:08:36: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:08:36: #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 03:08:36: #1 tags after filtering in treatment: 3898356 INFO @ Thu, 09 Dec 2021 03:08:36: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:08:36: #1 finished! INFO @ Thu, 09 Dec 2021 03:08:36: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:08:36: #2 number of paired peaks: 698 WARNING @ Thu, 09 Dec 2021 03:08:36: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Thu, 09 Dec 2021 03:08:36: start model_add_line... INFO @ Thu, 09 Dec 2021 03:08:36: start X-correlation... INFO @ Thu, 09 Dec 2021 03:08:36: end of X-cor INFO @ Thu, 09 Dec 2021 03:08:36: #2 finished! INFO @ Thu, 09 Dec 2021 03:08:36: #2 predicted fragment length is 223 bps INFO @ Thu, 09 Dec 2021 03:08:36: #2 alternative fragment length(s) may be 223 bps INFO @ Thu, 09 Dec 2021 03:08:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.05_model.r WARNING @ Thu, 09 Dec 2021 03:08:36: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:08:36: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Thu, 09 Dec 2021 03:08:36: #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 03:08:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:08:37: 6000000 INFO @ Thu, 09 Dec 2021 03:08:40: 10000000 INFO @ Thu, 09 Dec 2021 03:08:46: 7000000 INFO @ Thu, 09 Dec 2021 03:08:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:08:49: 11000000 INFO @ Thu, 09 Dec 2021 03:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.05_summits.bed INFO @ Thu, 09 Dec 2021 03:08:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (526 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:08:55: 8000000 INFO @ Thu, 09 Dec 2021 03:08:59: 12000000 INFO @ Thu, 09 Dec 2021 03:09:04: 9000000 INFO @ Thu, 09 Dec 2021 03:09:08: 13000000 INFO @ Thu, 09 Dec 2021 03:09:13: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:09:13: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:09:13: #1 total tags in treatment: 4350615 INFO @ Thu, 09 Dec 2021 03:09:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:09:13: #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 03:09:13: #1 tags after filtering in treatment: 3898356 INFO @ Thu, 09 Dec 2021 03:09:13: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:09:13: #1 finished! INFO @ Thu, 09 Dec 2021 03:09:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:09:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:09:13: #2 number of paired peaks: 698 WARNING @ Thu, 09 Dec 2021 03:09:13: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Thu, 09 Dec 2021 03:09:13: start model_add_line... INFO @ Thu, 09 Dec 2021 03:09:13: start X-correlation... INFO @ Thu, 09 Dec 2021 03:09:13: end of X-cor INFO @ Thu, 09 Dec 2021 03:09:13: #2 finished! INFO @ Thu, 09 Dec 2021 03:09:13: #2 predicted fragment length is 223 bps INFO @ Thu, 09 Dec 2021 03:09:13: #2 alternative fragment length(s) may be 223 bps INFO @ Thu, 09 Dec 2021 03:09:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.10_model.r WARNING @ Thu, 09 Dec 2021 03:09:13: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:09:13: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Thu, 09 Dec 2021 03:09:13: #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 03:09:13: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:09:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:09:14: 10000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:09:22: 11000000 INFO @ Thu, 09 Dec 2021 03:09:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:09:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:09:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:09:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.10_summits.bed INFO @ Thu, 09 Dec 2021 03:09:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (355 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:09:29: 12000000 INFO @ Thu, 09 Dec 2021 03:09:37: 13000000 INFO @ Thu, 09 Dec 2021 03:09:40: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:09:40: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:09:40: #1 total tags in treatment: 4350615 INFO @ Thu, 09 Dec 2021 03:09:40: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:09:40: #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 03:09:41: #1 tags after filtering in treatment: 3898356 INFO @ Thu, 09 Dec 2021 03:09:41: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:09:41: #1 finished! INFO @ Thu, 09 Dec 2021 03:09:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:09:41: #2 number of paired peaks: 698 WARNING @ Thu, 09 Dec 2021 03:09:41: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Thu, 09 Dec 2021 03:09:41: start model_add_line... INFO @ Thu, 09 Dec 2021 03:09:41: start X-correlation... INFO @ Thu, 09 Dec 2021 03:09:41: end of X-cor INFO @ Thu, 09 Dec 2021 03:09:41: #2 finished! INFO @ Thu, 09 Dec 2021 03:09:41: #2 predicted fragment length is 223 bps INFO @ Thu, 09 Dec 2021 03:09:41: #2 alternative fragment length(s) may be 223 bps INFO @ Thu, 09 Dec 2021 03:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.20_model.r WARNING @ Thu, 09 Dec 2021 03:09:41: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:09:41: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Thu, 09 Dec 2021 03:09:41: #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 03:09:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:09:50: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567189/SRX9567189.20_summits.bed INFO @ Thu, 09 Dec 2021 03:09:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling