Job ID = 14158506 SRX = SRX10641220 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:26 15457527 reads; of these: 15457527 (100.00%) were paired; of these: 9166013 (59.30%) aligned concordantly 0 times 5250702 (33.97%) aligned concordantly exactly 1 time 1040812 (6.73%) aligned concordantly >1 times ---- 9166013 pairs aligned concordantly 0 times; of these: 2664127 (29.07%) aligned discordantly 1 time ---- 6501886 pairs aligned 0 times concordantly or discordantly; of these: 13003772 mates make up the pairs; of these: 11734837 (90.24%) aligned 0 times 694897 (5.34%) aligned exactly 1 time 574038 (4.41%) aligned >1 times 62.04% overall alignment rate Time searching: 00:22:26 Overall time: 00:22:26 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] 1077831 / 8924156 = 0.1208 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 18:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.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 18:14:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:14:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:14:36: 1000000 INFO @ Wed, 08 Dec 2021 18:14:44: 2000000 INFO @ Wed, 08 Dec 2021 18:14:52: 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 @ Wed, 08 Dec 2021 18:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.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 18:14:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:14:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:15:02: 4000000 INFO @ Wed, 08 Dec 2021 18:15:10: 1000000 INFO @ Wed, 08 Dec 2021 18:15:12: 5000000 INFO @ Wed, 08 Dec 2021 18:15:22: 2000000 INFO @ Wed, 08 Dec 2021 18:15:23: 6000000 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 18:15:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.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 18:15:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:15:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:15:33: 7000000 INFO @ Wed, 08 Dec 2021 18:15:34: 3000000 INFO @ Wed, 08 Dec 2021 18:15:38: 1000000 INFO @ Wed, 08 Dec 2021 18:15:44: 8000000 INFO @ Wed, 08 Dec 2021 18:15:46: 4000000 INFO @ Wed, 08 Dec 2021 18:15:49: 2000000 INFO @ Wed, 08 Dec 2021 18:15:55: 9000000 INFO @ Wed, 08 Dec 2021 18:15:59: 5000000 INFO @ Wed, 08 Dec 2021 18:16:00: 3000000 INFO @ Wed, 08 Dec 2021 18:16:06: 10000000 INFO @ Wed, 08 Dec 2021 18:16:11: 4000000 INFO @ Wed, 08 Dec 2021 18:16:11: 6000000 INFO @ Wed, 08 Dec 2021 18:16:17: 11000000 INFO @ Wed, 08 Dec 2021 18:16:22: 5000000 INFO @ Wed, 08 Dec 2021 18:16:23: 7000000 INFO @ Wed, 08 Dec 2021 18:16:28: 12000000 INFO @ Wed, 08 Dec 2021 18:16:33: 6000000 INFO @ Wed, 08 Dec 2021 18:16:36: 8000000 INFO @ Wed, 08 Dec 2021 18:16:39: 13000000 INFO @ Wed, 08 Dec 2021 18:16:43: 7000000 INFO @ Wed, 08 Dec 2021 18:16:48: 9000000 INFO @ Wed, 08 Dec 2021 18:16:49: 14000000 INFO @ Wed, 08 Dec 2021 18:16:54: 8000000 INFO @ Wed, 08 Dec 2021 18:17:00: 15000000 INFO @ Wed, 08 Dec 2021 18:17:00: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:17:05: 9000000 INFO @ Wed, 08 Dec 2021 18:17:11: 16000000 INFO @ Wed, 08 Dec 2021 18:17:13: 11000000 INFO @ Wed, 08 Dec 2021 18:17:16: 10000000 INFO @ Wed, 08 Dec 2021 18:17:22: 17000000 INFO @ Wed, 08 Dec 2021 18:17:22: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:17:22: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:17:22: #1 total tags in treatment: 5459388 INFO @ Wed, 08 Dec 2021 18:17:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:17:22: #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 18:17:22: #1 tags after filtering in treatment: 4972677 INFO @ Wed, 08 Dec 2021 18:17:22: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:17:22: #1 finished! INFO @ Wed, 08 Dec 2021 18:17:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:17:23: #2 number of paired peaks: 623 WARNING @ Wed, 08 Dec 2021 18:17:23: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Wed, 08 Dec 2021 18:17:23: start model_add_line... INFO @ Wed, 08 Dec 2021 18:17:23: start X-correlation... INFO @ Wed, 08 Dec 2021 18:17:23: end of X-cor INFO @ Wed, 08 Dec 2021 18:17:23: #2 finished! INFO @ Wed, 08 Dec 2021 18:17:23: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 18:17:23: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 18:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.05_model.r WARNING @ Wed, 08 Dec 2021 18:17:23: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:17:23: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Wed, 08 Dec 2021 18:17:23: #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 18:17:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:17:25: 12000000 INFO @ Wed, 08 Dec 2021 18:17:27: 11000000 INFO @ Wed, 08 Dec 2021 18:17:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:17:37: 13000000 INFO @ Wed, 08 Dec 2021 18:17:37: 12000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:17:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:17:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:17:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.05_summits.bed INFO @ Wed, 08 Dec 2021 18:17:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:17:47: 13000000 INFO @ Wed, 08 Dec 2021 18:17:49: 14000000 INFO @ Wed, 08 Dec 2021 18:17:58: 14000000 INFO @ Wed, 08 Dec 2021 18:18:02: 15000000 INFO @ Wed, 08 Dec 2021 18:18:08: 15000000 INFO @ Wed, 08 Dec 2021 18:18:14: 16000000 INFO @ Wed, 08 Dec 2021 18:18:19: 16000000 INFO @ Wed, 08 Dec 2021 18:18:26: 17000000 INFO @ Wed, 08 Dec 2021 18:18:26: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:18:26: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:18:26: #1 total tags in treatment: 5459388 INFO @ Wed, 08 Dec 2021 18:18:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:18:26: #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 18:18:26: #1 tags after filtering in treatment: 4972677 INFO @ Wed, 08 Dec 2021 18:18:26: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:18:26: #1 finished! INFO @ Wed, 08 Dec 2021 18:18:26: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:18:27: #2 number of paired peaks: 623 WARNING @ Wed, 08 Dec 2021 18:18:27: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Wed, 08 Dec 2021 18:18:27: start model_add_line... INFO @ Wed, 08 Dec 2021 18:18:27: start X-correlation... INFO @ Wed, 08 Dec 2021 18:18:27: end of X-cor INFO @ Wed, 08 Dec 2021 18:18:27: #2 finished! INFO @ Wed, 08 Dec 2021 18:18:27: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 18:18:27: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 18:18:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.10_model.r WARNING @ Wed, 08 Dec 2021 18:18:27: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:18:27: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Wed, 08 Dec 2021 18:18:27: #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 18:18:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:18:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:18:29: 17000000 INFO @ Wed, 08 Dec 2021 18:18:29: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:18:29: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:18:29: #1 total tags in treatment: 5459388 INFO @ Wed, 08 Dec 2021 18:18:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:18:29: #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 18:18:29: #1 tags after filtering in treatment: 4972677 INFO @ Wed, 08 Dec 2021 18:18:29: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:18:29: #1 finished! INFO @ Wed, 08 Dec 2021 18:18:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:18:30: #2 number of paired peaks: 623 WARNING @ Wed, 08 Dec 2021 18:18:30: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Wed, 08 Dec 2021 18:18:30: start model_add_line... INFO @ Wed, 08 Dec 2021 18:18:30: start X-correlation... INFO @ Wed, 08 Dec 2021 18:18:30: end of X-cor INFO @ Wed, 08 Dec 2021 18:18:30: #2 finished! INFO @ Wed, 08 Dec 2021 18:18:30: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 18:18:30: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 18:18:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.20_model.r WARNING @ Wed, 08 Dec 2021 18:18:30: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:18:30: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Wed, 08 Dec 2021 18:18:30: #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 18:18:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:18:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:18:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.10_summits.bed INFO @ Wed, 08 Dec 2021 18:18:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (355 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:18:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:18:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:18:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641220/SRX10641220.20_summits.bed INFO @ Wed, 08 Dec 2021 18:18:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 8 millis CompletedMACS2peakCalling