Job ID = 8070464 SRX = SRX8392421 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: 00:15:08 9449036 reads; of these: 9449036 (100.00%) were paired; of these: 3638265 (38.50%) aligned concordantly 0 times 4910147 (51.96%) aligned concordantly exactly 1 time 900624 (9.53%) aligned concordantly >1 times ---- 3638265 pairs aligned concordantly 0 times; of these: 1200575 (33.00%) aligned discordantly 1 time ---- 2437690 pairs aligned 0 times concordantly or discordantly; of these: 4875380 mates make up the pairs; of these: 4470616 (91.70%) aligned 0 times 174355 (3.58%) aligned exactly 1 time 230409 (4.73%) aligned >1 times 76.34% overall alignment rate Time searching: 00:15:08 Overall time: 00:15:08 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 12 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] 1512109 / 6942656 = 0.2178 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.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, 08 Aug 2020 13:27:19: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:19: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:25: 1000000 INFO @ Sat, 08 Aug 2020 13:27:32: 2000000 INFO @ Sat, 08 Aug 2020 13:27:38: 3000000 INFO @ Sat, 08 Aug 2020 13:27:45: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:27:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.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, 08 Aug 2020 13:27:49: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:49: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:51: 5000000 INFO @ Sat, 08 Aug 2020 13:27:56: 1000000 INFO @ Sat, 08 Aug 2020 13:27:58: 6000000 INFO @ Sat, 08 Aug 2020 13:28:03: 2000000 INFO @ Sat, 08 Aug 2020 13:28:06: 7000000 INFO @ Sat, 08 Aug 2020 13:28:10: 3000000 INFO @ Sat, 08 Aug 2020 13:28:13: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:28:18: 4000000 INFO @ Sat, 08 Aug 2020 13:28:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.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, 08 Aug 2020 13:28:19: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:28:19: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:28:20: 9000000 INFO @ Sat, 08 Aug 2020 13:28:25: 5000000 INFO @ Sat, 08 Aug 2020 13:28:26: 1000000 INFO @ Sat, 08 Aug 2020 13:28:27: 10000000 INFO @ Sat, 08 Aug 2020 13:28:33: 6000000 INFO @ Sat, 08 Aug 2020 13:28:34: 2000000 INFO @ Sat, 08 Aug 2020 13:28:34: 11000000 INFO @ Sat, 08 Aug 2020 13:28:37: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:37: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:37: #1 total tags in treatment: 4512316 INFO @ Sat, 08 Aug 2020 13:28:37: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:28:37: #1 tags after filtering in treatment: 4147110 INFO @ Sat, 08 Aug 2020 13:28:37: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:28:37: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:37: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:37: #2 number of paired peaks: 517 WARNING @ Sat, 08 Aug 2020 13:28:37: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 08 Aug 2020 13:28:37: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:37: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:38: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:38: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:38: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:28:38: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:28:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.05_model.r WARNING @ Sat, 08 Aug 2020 13:28:38: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:38: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:28:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:28:38: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:40: 7000000 INFO @ Sat, 08 Aug 2020 13:28:41: 3000000 INFO @ Sat, 08 Aug 2020 13:28:47: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:47: 8000000 INFO @ Sat, 08 Aug 2020 13:28:48: 4000000 INFO @ Sat, 08 Aug 2020 13:28:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.05_summits.bed INFO @ Sat, 08 Aug 2020 13:28:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (652 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:28:55: 9000000 INFO @ Sat, 08 Aug 2020 13:28:55: 5000000 INFO @ Sat, 08 Aug 2020 13:29:02: 10000000 INFO @ Sat, 08 Aug 2020 13:29:02: 6000000 INFO @ Sat, 08 Aug 2020 13:29:09: 11000000 INFO @ Sat, 08 Aug 2020 13:29:09: 7000000 INFO @ Sat, 08 Aug 2020 13:29:12: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:29:12: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:29:12: #1 total tags in treatment: 4512316 INFO @ Sat, 08 Aug 2020 13:29:12: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:29:12: #1 tags after filtering in treatment: 4147110 INFO @ Sat, 08 Aug 2020 13:29:12: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:29:12: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:12: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:12: #2 number of paired peaks: 517 WARNING @ Sat, 08 Aug 2020 13:29:12: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 08 Aug 2020 13:29:12: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:12: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:12: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:12: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:12: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:29:12: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:29:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.10_model.r WARNING @ Sat, 08 Aug 2020 13:29:12: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:29:12: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:29:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:29:12: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:29:16: 8000000 INFO @ Sat, 08 Aug 2020 13:29:22: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:23: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:29:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.10_summits.bed INFO @ Sat, 08 Aug 2020 13:29:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (297 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:29:30: 10000000 INFO @ Sat, 08 Aug 2020 13:29:36: 11000000 INFO @ Sat, 08 Aug 2020 13:29:39: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:29:39: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:29:39: #1 total tags in treatment: 4512316 INFO @ Sat, 08 Aug 2020 13:29:39: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:29:39: #1 tags after filtering in treatment: 4147110 INFO @ Sat, 08 Aug 2020 13:29:39: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:29:39: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:39: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:39: #2 number of paired peaks: 517 WARNING @ Sat, 08 Aug 2020 13:29:39: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 08 Aug 2020 13:29:39: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:39: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:39: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:39: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:39: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:29:39: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:29:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.20_model.r WARNING @ Sat, 08 Aug 2020 13:29:39: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:29:39: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:29:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:29:39: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:29:49: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392421/SRX8392421.20_summits.bed INFO @ Sat, 08 Aug 2020 13:29:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling