Job ID = 12265410 SRX = SRX7687153 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: 00:32:40 27001433 reads; of these: 27001433 (100.00%) were paired; of these: 5906204 (21.87%) aligned concordantly 0 times 18587693 (68.84%) aligned concordantly exactly 1 time 2507536 (9.29%) aligned concordantly >1 times ---- 5906204 pairs aligned concordantly 0 times; of these: 2866380 (48.53%) aligned discordantly 1 time ---- 3039824 pairs aligned 0 times concordantly or discordantly; of these: 6079648 mates make up the pairs; of these: 5174904 (85.12%) aligned 0 times 401528 (6.60%) aligned exactly 1 time 503216 (8.28%) aligned >1 times 90.42% overall alignment rate Time searching: 00:32:40 Overall time: 00:32:40 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 20 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] 14170264 / 23915686 = 0.5925 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:37:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.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, 03 Apr 2021 07:37:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:37:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:37:40: 1000000 INFO @ Sat, 03 Apr 2021 07:37:45: 2000000 INFO @ Sat, 03 Apr 2021 07:37:52: 3000000 INFO @ Sat, 03 Apr 2021 07:37:58: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:38:04: 5000000 INFO @ Sat, 03 Apr 2021 07:38:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.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, 03 Apr 2021 07:38:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:38:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:38:10: 6000000 INFO @ Sat, 03 Apr 2021 07:38:11: 1000000 INFO @ Sat, 03 Apr 2021 07:38:16: 7000000 INFO @ Sat, 03 Apr 2021 07:38:18: 2000000 INFO @ Sat, 03 Apr 2021 07:38:22: 8000000 INFO @ Sat, 03 Apr 2021 07:38:26: 3000000 INFO @ Sat, 03 Apr 2021 07:38:28: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:38:34: 4000000 INFO @ Sat, 03 Apr 2021 07:38:34: 10000000 INFO @ Sat, 03 Apr 2021 07:38:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.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, 03 Apr 2021 07:38:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:38:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:38:40: 11000000 INFO @ Sat, 03 Apr 2021 07:38:42: 5000000 INFO @ Sat, 03 Apr 2021 07:38:42: 1000000 INFO @ Sat, 03 Apr 2021 07:38:46: 12000000 INFO @ Sat, 03 Apr 2021 07:38:51: 6000000 INFO @ Sat, 03 Apr 2021 07:38:52: 2000000 INFO @ Sat, 03 Apr 2021 07:38:52: 13000000 INFO @ Sat, 03 Apr 2021 07:38:58: 14000000 INFO @ Sat, 03 Apr 2021 07:39:00: 7000000 INFO @ Sat, 03 Apr 2021 07:39:00: 3000000 INFO @ Sat, 03 Apr 2021 07:39:04: 15000000 INFO @ Sat, 03 Apr 2021 07:39:08: 8000000 INFO @ Sat, 03 Apr 2021 07:39:09: 4000000 INFO @ Sat, 03 Apr 2021 07:39:10: 16000000 INFO @ Sat, 03 Apr 2021 07:39:16: 17000000 INFO @ Sat, 03 Apr 2021 07:39:17: 9000000 INFO @ Sat, 03 Apr 2021 07:39:17: 5000000 INFO @ Sat, 03 Apr 2021 07:39:22: 18000000 INFO @ Sat, 03 Apr 2021 07:39:25: 10000000 INFO @ Sat, 03 Apr 2021 07:39:26: 6000000 INFO @ Sat, 03 Apr 2021 07:39:28: 19000000 INFO @ Sat, 03 Apr 2021 07:39:34: 11000000 INFO @ Sat, 03 Apr 2021 07:39:34: 7000000 INFO @ Sat, 03 Apr 2021 07:39:35: 20000000 INFO @ Sat, 03 Apr 2021 07:39:38: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:39:38: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:39:38: #1 total tags in treatment: 8514302 INFO @ Sat, 03 Apr 2021 07:39:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:39:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:39:38: #1 tags after filtering in treatment: 6547196 INFO @ Sat, 03 Apr 2021 07:39:38: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 07:39:38: #1 finished! INFO @ Sat, 03 Apr 2021 07:39:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:39:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:39:39: #2 number of paired peaks: 430 WARNING @ Sat, 03 Apr 2021 07:39:39: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Sat, 03 Apr 2021 07:39:39: start model_add_line... INFO @ Sat, 03 Apr 2021 07:39:39: start X-correlation... INFO @ Sat, 03 Apr 2021 07:39:39: end of X-cor INFO @ Sat, 03 Apr 2021 07:39:39: #2 finished! INFO @ Sat, 03 Apr 2021 07:39:39: #2 predicted fragment length is 129 bps INFO @ Sat, 03 Apr 2021 07:39:39: #2 alternative fragment length(s) may be 4,129,147,166 bps INFO @ Sat, 03 Apr 2021 07:39:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.05_model.r WARNING @ Sat, 03 Apr 2021 07:39:39: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:39:39: #2 You may need to consider one of the other alternative d(s): 4,129,147,166 WARNING @ Sat, 03 Apr 2021 07:39:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:39:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:39:42: 12000000 INFO @ Sat, 03 Apr 2021 07:39:43: 8000000 INFO @ Sat, 03 Apr 2021 07:39:50: 13000000 INFO @ Sat, 03 Apr 2021 07:39:51: 9000000 INFO @ Sat, 03 Apr 2021 07:39:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:39:58: 14000000 INFO @ Sat, 03 Apr 2021 07:39:59: 10000000 INFO @ Sat, 03 Apr 2021 07:40:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:40:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:40:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.05_summits.bed INFO @ Sat, 03 Apr 2021 07:40:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (991 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:40:06: 15000000 INFO @ Sat, 03 Apr 2021 07:40:07: 11000000 INFO @ Sat, 03 Apr 2021 07:40:14: 16000000 INFO @ Sat, 03 Apr 2021 07:40:15: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:40:22: 17000000 INFO @ Sat, 03 Apr 2021 07:40:23: 13000000 INFO @ Sat, 03 Apr 2021 07:40:29: 18000000 INFO @ Sat, 03 Apr 2021 07:40:31: 14000000 INFO @ Sat, 03 Apr 2021 07:40:36: 19000000 INFO @ Sat, 03 Apr 2021 07:40:38: 15000000 INFO @ Sat, 03 Apr 2021 07:40:43: 20000000 INFO @ Sat, 03 Apr 2021 07:40:46: 16000000 INFO @ Sat, 03 Apr 2021 07:40:46: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:40:46: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:40:46: #1 total tags in treatment: 8514302 INFO @ Sat, 03 Apr 2021 07:40:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:40:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:40:46: #1 tags after filtering in treatment: 6547196 INFO @ Sat, 03 Apr 2021 07:40:46: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 07:40:46: #1 finished! INFO @ Sat, 03 Apr 2021 07:40:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:40:46: #2 number of paired peaks: 430 WARNING @ Sat, 03 Apr 2021 07:40:46: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Sat, 03 Apr 2021 07:40:46: start model_add_line... INFO @ Sat, 03 Apr 2021 07:40:47: start X-correlation... INFO @ Sat, 03 Apr 2021 07:40:47: end of X-cor INFO @ Sat, 03 Apr 2021 07:40:47: #2 finished! INFO @ Sat, 03 Apr 2021 07:40:47: #2 predicted fragment length is 129 bps INFO @ Sat, 03 Apr 2021 07:40:47: #2 alternative fragment length(s) may be 4,129,147,166 bps INFO @ Sat, 03 Apr 2021 07:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.10_model.r WARNING @ Sat, 03 Apr 2021 07:40:47: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:40:47: #2 You may need to consider one of the other alternative d(s): 4,129,147,166 WARNING @ Sat, 03 Apr 2021 07:40:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:40:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:40:53: 17000000 INFO @ Sat, 03 Apr 2021 07:41:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:41:01: 18000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:41:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:41:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:41:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.10_summits.bed INFO @ Sat, 03 Apr 2021 07:41:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (456 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:41:08: 19000000 INFO @ Sat, 03 Apr 2021 07:41:15: 20000000 INFO @ Sat, 03 Apr 2021 07:41:18: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:41:18: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:41:18: #1 total tags in treatment: 8514302 INFO @ Sat, 03 Apr 2021 07:41:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:41:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:41:18: #1 tags after filtering in treatment: 6547196 INFO @ Sat, 03 Apr 2021 07:41:18: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 07:41:18: #1 finished! INFO @ Sat, 03 Apr 2021 07:41:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:41:19: #2 number of paired peaks: 430 WARNING @ Sat, 03 Apr 2021 07:41:19: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Sat, 03 Apr 2021 07:41:19: start model_add_line... INFO @ Sat, 03 Apr 2021 07:41:19: start X-correlation... INFO @ Sat, 03 Apr 2021 07:41:19: end of X-cor INFO @ Sat, 03 Apr 2021 07:41:19: #2 finished! INFO @ Sat, 03 Apr 2021 07:41:19: #2 predicted fragment length is 129 bps INFO @ Sat, 03 Apr 2021 07:41:19: #2 alternative fragment length(s) may be 4,129,147,166 bps INFO @ Sat, 03 Apr 2021 07:41:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.20_model.r WARNING @ Sat, 03 Apr 2021 07:41:19: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:41:19: #2 You may need to consider one of the other alternative d(s): 4,129,147,166 WARNING @ Sat, 03 Apr 2021 07:41:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:41:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:41:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:41:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:41:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:41:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:41:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687153/SRX7687153.20_summits.bed INFO @ Sat, 03 Apr 2021 07:41:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 7 millis CompletedMACS2peakCalling