Job ID = 14157939 SRX = SRX10641209 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16904509 spots for SRR14280069/SRR14280069.sra Written 16904509 spots for SRR14280069/SRR14280069.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158203 ("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: 00:22:32 16904509 reads; of these: 16904509 (100.00%) were paired; of these: 11465981 (67.83%) aligned concordantly 0 times 4483788 (26.52%) aligned concordantly exactly 1 time 954740 (5.65%) aligned concordantly >1 times ---- 11465981 pairs aligned concordantly 0 times; of these: 2909666 (25.38%) aligned discordantly 1 time ---- 8556315 pairs aligned 0 times concordantly or discordantly; of these: 17112630 mates make up the pairs; of these: 15595956 (91.14%) aligned 0 times 836501 (4.89%) aligned exactly 1 time 680173 (3.97%) aligned >1 times 53.87% overall alignment rate Time searching: 00:22:32 Overall time: 00:22:32 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 16 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] 1122182 / 8326105 = 0.1348 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 @ Wed, 08 Dec 2021 13:29:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.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 @ Wed, 08 Dec 2021 13:29:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:29:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:29:32: 1000000 INFO @ Wed, 08 Dec 2021 13:29:42: 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 @ Wed, 08 Dec 2021 13:29:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.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 @ Wed, 08 Dec 2021 13:29:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:29:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:29:52: 3000000 INFO @ Wed, 08 Dec 2021 13:30:01: 4000000 INFO @ Wed, 08 Dec 2021 13:30:02: 1000000 INFO @ Wed, 08 Dec 2021 13:30:11: 5000000 INFO @ Wed, 08 Dec 2021 13:30:11: 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 @ Wed, 08 Dec 2021 13:30:21: 3000000 INFO @ Wed, 08 Dec 2021 13:30:22: 6000000 INFO @ Wed, 08 Dec 2021 13:30:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.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 @ Wed, 08 Dec 2021 13:30:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:30:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:30:32: 4000000 INFO @ Wed, 08 Dec 2021 13:30:32: 1000000 INFO @ Wed, 08 Dec 2021 13:30:33: 7000000 INFO @ Wed, 08 Dec 2021 13:30:42: 2000000 INFO @ Wed, 08 Dec 2021 13:30:42: 5000000 INFO @ Wed, 08 Dec 2021 13:30:44: 8000000 INFO @ Wed, 08 Dec 2021 13:30:52: 3000000 INFO @ Wed, 08 Dec 2021 13:30:52: 6000000 INFO @ Wed, 08 Dec 2021 13:30:55: 9000000 INFO @ Wed, 08 Dec 2021 13:31:02: 7000000 INFO @ Wed, 08 Dec 2021 13:31:03: 4000000 INFO @ Wed, 08 Dec 2021 13:31:07: 10000000 INFO @ Wed, 08 Dec 2021 13:31:12: 8000000 INFO @ Wed, 08 Dec 2021 13:31:13: 5000000 INFO @ Wed, 08 Dec 2021 13:31:18: 11000000 INFO @ Wed, 08 Dec 2021 13:31:22: 9000000 INFO @ Wed, 08 Dec 2021 13:31:23: 6000000 INFO @ Wed, 08 Dec 2021 13:31:29: 12000000 INFO @ Wed, 08 Dec 2021 13:31:32: 10000000 INFO @ Wed, 08 Dec 2021 13:31:33: 7000000 INFO @ Wed, 08 Dec 2021 13:31:40: 13000000 INFO @ Wed, 08 Dec 2021 13:31:42: 11000000 INFO @ Wed, 08 Dec 2021 13:31:43: 8000000 INFO @ Wed, 08 Dec 2021 13:31:51: 14000000 INFO @ Wed, 08 Dec 2021 13:31:52: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:31:53: 9000000 INFO @ Wed, 08 Dec 2021 13:32:02: 13000000 INFO @ Wed, 08 Dec 2021 13:32:02: 15000000 INFO @ Wed, 08 Dec 2021 13:32:03: 10000000 INFO @ Wed, 08 Dec 2021 13:32:12: 14000000 INFO @ Wed, 08 Dec 2021 13:32:13: 11000000 INFO @ Wed, 08 Dec 2021 13:32:13: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:32:13: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:32:13: #1 total tags in treatment: 4623725 INFO @ Wed, 08 Dec 2021 13:32:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:32:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 13:32:13: #1 tags after filtering in treatment: 4300974 INFO @ Wed, 08 Dec 2021 13:32:13: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:32:13: #1 finished! INFO @ Wed, 08 Dec 2021 13:32:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:32:14: #2 number of paired peaks: 636 WARNING @ Wed, 08 Dec 2021 13:32:14: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Wed, 08 Dec 2021 13:32:14: start model_add_line... INFO @ Wed, 08 Dec 2021 13:32:14: start X-correlation... INFO @ Wed, 08 Dec 2021 13:32:14: end of X-cor INFO @ Wed, 08 Dec 2021 13:32:14: #2 finished! INFO @ Wed, 08 Dec 2021 13:32:14: #2 predicted fragment length is 221 bps INFO @ Wed, 08 Dec 2021 13:32:14: #2 alternative fragment length(s) may be 221 bps INFO @ Wed, 08 Dec 2021 13:32:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.05_model.r WARNING @ Wed, 08 Dec 2021 13:32:14: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:32:14: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Wed, 08 Dec 2021 13:32:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 13:32:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:32:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:32:21: 15000000 INFO @ Wed, 08 Dec 2021 13:32:23: 12000000 INFO @ Wed, 08 Dec 2021 13:32:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.05_summits.bed INFO @ Wed, 08 Dec 2021 13:32:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (419 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:32:30: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:32:30: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:32:30: #1 total tags in treatment: 4623725 INFO @ Wed, 08 Dec 2021 13:32:30: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:32:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 13:32:31: #1 tags after filtering in treatment: 4300974 INFO @ Wed, 08 Dec 2021 13:32:31: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:32:31: #1 finished! INFO @ Wed, 08 Dec 2021 13:32:31: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:32:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:32:31: #2 number of paired peaks: 636 WARNING @ Wed, 08 Dec 2021 13:32:31: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Wed, 08 Dec 2021 13:32:31: start model_add_line... INFO @ Wed, 08 Dec 2021 13:32:31: start X-correlation... INFO @ Wed, 08 Dec 2021 13:32:31: end of X-cor INFO @ Wed, 08 Dec 2021 13:32:31: #2 finished! INFO @ Wed, 08 Dec 2021 13:32:31: #2 predicted fragment length is 221 bps INFO @ Wed, 08 Dec 2021 13:32:31: #2 alternative fragment length(s) may be 221 bps INFO @ Wed, 08 Dec 2021 13:32:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.10_model.r WARNING @ Wed, 08 Dec 2021 13:32:31: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:32:31: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Wed, 08 Dec 2021 13:32:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 13:32:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:32:32: 13000000 INFO @ Wed, 08 Dec 2021 13:32:40: 14000000 INFO @ Wed, 08 Dec 2021 13:32:42: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:32:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:32:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.10_summits.bed INFO @ Wed, 08 Dec 2021 13:32:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:32:48: 15000000 INFO @ Wed, 08 Dec 2021 13:32:56: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:32:56: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:32:56: #1 total tags in treatment: 4623725 INFO @ Wed, 08 Dec 2021 13:32:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:32:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 13:32:56: #1 tags after filtering in treatment: 4300974 INFO @ Wed, 08 Dec 2021 13:32:56: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:32:56: #1 finished! INFO @ Wed, 08 Dec 2021 13:32:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:32:56: #2 number of paired peaks: 636 WARNING @ Wed, 08 Dec 2021 13:32:56: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Wed, 08 Dec 2021 13:32:56: start model_add_line... INFO @ Wed, 08 Dec 2021 13:32:56: start X-correlation... INFO @ Wed, 08 Dec 2021 13:32:56: end of X-cor INFO @ Wed, 08 Dec 2021 13:32:56: #2 finished! INFO @ Wed, 08 Dec 2021 13:32:56: #2 predicted fragment length is 221 bps INFO @ Wed, 08 Dec 2021 13:32:56: #2 alternative fragment length(s) may be 221 bps INFO @ Wed, 08 Dec 2021 13:32:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.20_model.r WARNING @ Wed, 08 Dec 2021 13:32:56: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:32:56: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Wed, 08 Dec 2021 13:32:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 13:32:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:33:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641209/SRX10641209.20_summits.bed INFO @ Wed, 08 Dec 2021 13:33:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 1 millis CompletedMACS2peakCalling