Job ID = 14160639 SRX = SRX9567188 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: 00:46:22 26401687 reads; of these: 26401687 (100.00%) were paired; of these: 10850043 (41.10%) aligned concordantly 0 times 13463548 (51.00%) aligned concordantly exactly 1 time 2088096 (7.91%) aligned concordantly >1 times ---- 10850043 pairs aligned concordantly 0 times; of these: 4745584 (43.74%) aligned discordantly 1 time ---- 6104459 pairs aligned 0 times concordantly or discordantly; of these: 12208918 mates make up the pairs; of these: 9877071 (80.90%) aligned 0 times 1199080 (9.82%) aligned exactly 1 time 1132767 (9.28%) aligned >1 times 81.29% overall alignment rate Time searching: 00:46:22 Overall time: 00:46:22 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 32 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] 16491732 / 20273388 = 0.8135 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 04:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.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 04:27:01: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:27:01: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:27:09: 1000000 INFO @ Thu, 09 Dec 2021 04:27:17: 2000000 INFO @ Thu, 09 Dec 2021 04:27:25: 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 04:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.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 04:27:31: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:27:31: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:27:33: 4000000 INFO @ Thu, 09 Dec 2021 04:27:44: 1000000 INFO @ Thu, 09 Dec 2021 04:27:44: 5000000 INFO @ Thu, 09 Dec 2021 04:27:55: 6000000 INFO @ Thu, 09 Dec 2021 04:27:57: 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 @ Thu, 09 Dec 2021 04:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.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 04:28:01: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:28:01: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:28:07: 7000000 INFO @ Thu, 09 Dec 2021 04:28:09: 3000000 INFO @ Thu, 09 Dec 2021 04:28:14: 1000000 INFO @ Thu, 09 Dec 2021 04:28:18: 8000000 INFO @ Thu, 09 Dec 2021 04:28:22: 4000000 INFO @ Thu, 09 Dec 2021 04:28:28: 2000000 INFO @ Thu, 09 Dec 2021 04:28:29: 9000000 INFO @ Thu, 09 Dec 2021 04:28:35: 5000000 INFO @ Thu, 09 Dec 2021 04:28:40: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:28:40: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:28:40: #1 total tags in treatment: 2923250 INFO @ Thu, 09 Dec 2021 04:28:40: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:28:40: #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 04:28:40: #1 tags after filtering in treatment: 2615046 INFO @ Thu, 09 Dec 2021 04:28:40: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 04:28:40: #1 finished! INFO @ Thu, 09 Dec 2021 04:28:40: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:28:40: #2 number of paired peaks: 664 WARNING @ Thu, 09 Dec 2021 04:28:40: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Thu, 09 Dec 2021 04:28:40: start model_add_line... INFO @ Thu, 09 Dec 2021 04:28:40: start X-correlation... INFO @ Thu, 09 Dec 2021 04:28:40: end of X-cor INFO @ Thu, 09 Dec 2021 04:28:40: #2 finished! INFO @ Thu, 09 Dec 2021 04:28:40: #2 predicted fragment length is 232 bps INFO @ Thu, 09 Dec 2021 04:28:40: #2 alternative fragment length(s) may be 232 bps INFO @ Thu, 09 Dec 2021 04:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.05_model.r WARNING @ Thu, 09 Dec 2021 04:28:40: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:28:40: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Thu, 09 Dec 2021 04:28:40: #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 04:28:40: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:28:41: 3000000 INFO @ Thu, 09 Dec 2021 04:28:47: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:28:48: 6000000 INFO @ Thu, 09 Dec 2021 04:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.05_summits.bed INFO @ Thu, 09 Dec 2021 04:28:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (441 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:28:54: 4000000 INFO @ Thu, 09 Dec 2021 04:29:01: 7000000 INFO @ Thu, 09 Dec 2021 04:29:07: 5000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:29:13: 8000000 INFO @ Thu, 09 Dec 2021 04:29:20: 6000000 INFO @ Thu, 09 Dec 2021 04:29:26: 9000000 INFO @ Thu, 09 Dec 2021 04:29:32: 7000000 INFO @ Thu, 09 Dec 2021 04:29:38: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:29:38: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:29:38: #1 total tags in treatment: 2923250 INFO @ Thu, 09 Dec 2021 04:29:38: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:29:38: #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 04:29:38: #1 tags after filtering in treatment: 2615046 INFO @ Thu, 09 Dec 2021 04:29:38: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 04:29:38: #1 finished! INFO @ Thu, 09 Dec 2021 04:29:38: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:29:38: #2 number of paired peaks: 664 WARNING @ Thu, 09 Dec 2021 04:29:38: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Thu, 09 Dec 2021 04:29:38: start model_add_line... INFO @ Thu, 09 Dec 2021 04:29:38: start X-correlation... INFO @ Thu, 09 Dec 2021 04:29:38: end of X-cor INFO @ Thu, 09 Dec 2021 04:29:38: #2 finished! INFO @ Thu, 09 Dec 2021 04:29:38: #2 predicted fragment length is 232 bps INFO @ Thu, 09 Dec 2021 04:29:38: #2 alternative fragment length(s) may be 232 bps INFO @ Thu, 09 Dec 2021 04:29:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.10_model.r WARNING @ Thu, 09 Dec 2021 04:29:38: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:29:38: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Thu, 09 Dec 2021 04:29:38: #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 04:29:38: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:29:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:29:44: 8000000 INFO @ Thu, 09 Dec 2021 04:29:45: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.10_summits.bed INFO @ Thu, 09 Dec 2021 04:29:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (304 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:29:56: 9000000 INFO @ Thu, 09 Dec 2021 04:30:06: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:30:06: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:30:06: #1 total tags in treatment: 2923250 INFO @ Thu, 09 Dec 2021 04:30:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:30:06: #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 04:30:06: #1 tags after filtering in treatment: 2615046 INFO @ Thu, 09 Dec 2021 04:30:06: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 04:30:06: #1 finished! INFO @ Thu, 09 Dec 2021 04:30:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:30:06: #2 number of paired peaks: 664 WARNING @ Thu, 09 Dec 2021 04:30:06: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Thu, 09 Dec 2021 04:30:06: start model_add_line... INFO @ Thu, 09 Dec 2021 04:30:06: start X-correlation... INFO @ Thu, 09 Dec 2021 04:30:06: end of X-cor INFO @ Thu, 09 Dec 2021 04:30:06: #2 finished! INFO @ Thu, 09 Dec 2021 04:30:06: #2 predicted fragment length is 232 bps INFO @ Thu, 09 Dec 2021 04:30:06: #2 alternative fragment length(s) may be 232 bps INFO @ Thu, 09 Dec 2021 04:30:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.20_model.r WARNING @ Thu, 09 Dec 2021 04:30:06: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:30:06: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Thu, 09 Dec 2021 04:30:06: #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 04:30:06: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:30:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567188/SRX9567188.20_summits.bed INFO @ Thu, 09 Dec 2021 04:30:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis CompletedMACS2peakCalling