Job ID = 14158231 SRX = SRX10641207 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: 00:36:07 18394539 reads; of these: 18394539 (100.00%) were paired; of these: 10365509 (56.35%) aligned concordantly 0 times 6853781 (37.26%) aligned concordantly exactly 1 time 1175249 (6.39%) aligned concordantly >1 times ---- 10365509 pairs aligned concordantly 0 times; of these: 3071080 (29.63%) aligned discordantly 1 time ---- 7294429 pairs aligned 0 times concordantly or discordantly; of these: 14588858 mates make up the pairs; of these: 13164057 (90.23%) aligned 0 times 779709 (5.34%) aligned exactly 1 time 645092 (4.42%) aligned >1 times 64.22% overall alignment rate Time searching: 00:36:07 Overall time: 00:36:07 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] 1552569 / 11066556 = 0.1403 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 15:47:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.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 15:47:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:47:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:47:33: 1000000 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 15:47:46: 2000000 INFO @ Wed, 08 Dec 2021 15:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.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 15:47:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:47:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:48:00: 3000000 INFO @ Wed, 08 Dec 2021 15:48:02: 1000000 INFO @ Wed, 08 Dec 2021 15:48:14: 4000000 BedGraph に変換中... INFO @ Wed, 08 Dec 2021 15:48:16: 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 15:48:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.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 15:48:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:48:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:48:28: 5000000 INFO @ Wed, 08 Dec 2021 15:48:30: 3000000 INFO @ Wed, 08 Dec 2021 15:48:32: 1000000 INFO @ Wed, 08 Dec 2021 15:48:41: 6000000 INFO @ Wed, 08 Dec 2021 15:48:45: 2000000 INFO @ Wed, 08 Dec 2021 15:48:45: 4000000 INFO @ Wed, 08 Dec 2021 15:48:55: 7000000 INFO @ Wed, 08 Dec 2021 15:48:58: 3000000 INFO @ Wed, 08 Dec 2021 15:49:01: 5000000 INFO @ Wed, 08 Dec 2021 15:49:09: 8000000 INFO @ Wed, 08 Dec 2021 15:49:11: 4000000 INFO @ Wed, 08 Dec 2021 15:49:16: 6000000 INFO @ Wed, 08 Dec 2021 15:49:22: 9000000 INFO @ Wed, 08 Dec 2021 15:49:24: 5000000 INFO @ Wed, 08 Dec 2021 15:49:32: 7000000 INFO @ Wed, 08 Dec 2021 15:49:35: 10000000 INFO @ Wed, 08 Dec 2021 15:49:36: 6000000 INFO @ Wed, 08 Dec 2021 15:49:48: 8000000 INFO @ Wed, 08 Dec 2021 15:49:48: 11000000 INFO @ Wed, 08 Dec 2021 15:49:49: 7000000 INFO @ Wed, 08 Dec 2021 15:50:01: 12000000 INFO @ Wed, 08 Dec 2021 15:50:02: 8000000 INFO @ Wed, 08 Dec 2021 15:50:03: 9000000 INFO @ Wed, 08 Dec 2021 15:50:14: 13000000 INFO @ Wed, 08 Dec 2021 15:50:15: 9000000 INFO @ Wed, 08 Dec 2021 15:50:18: 10000000 INFO @ Wed, 08 Dec 2021 15:50:27: 10000000 INFO @ Wed, 08 Dec 2021 15:50:28: 14000000 INFO @ Wed, 08 Dec 2021 15:50:33: 11000000 INFO @ Wed, 08 Dec 2021 15:50:40: 11000000 INFO @ Wed, 08 Dec 2021 15:50:42: 15000000 INFO @ Wed, 08 Dec 2021 15:50:47: 12000000 INFO @ Wed, 08 Dec 2021 15:50:52: 12000000 INFO @ Wed, 08 Dec 2021 15:50:55: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:51:02: 13000000 INFO @ Wed, 08 Dec 2021 15:51:05: 13000000 INFO @ Wed, 08 Dec 2021 15:51:08: 17000000 INFO @ Wed, 08 Dec 2021 15:51:18: 14000000 INFO @ Wed, 08 Dec 2021 15:51:18: 14000000 INFO @ Wed, 08 Dec 2021 15:51:21: 18000000 INFO @ Wed, 08 Dec 2021 15:51:31: 15000000 INFO @ Wed, 08 Dec 2021 15:51:33: 15000000 INFO @ Wed, 08 Dec 2021 15:51:34: 19000000 INFO @ Wed, 08 Dec 2021 15:51:43: 16000000 INFO @ Wed, 08 Dec 2021 15:51:47: 20000000 INFO @ Wed, 08 Dec 2021 15:51:49: 16000000 INFO @ Wed, 08 Dec 2021 15:51:54: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:51:54: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:51:54: #1 total tags in treatment: 6819765 INFO @ Wed, 08 Dec 2021 15:51:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:51:54: #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 15:51:55: #1 tags after filtering in treatment: 6401734 INFO @ Wed, 08 Dec 2021 15:51:55: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 15:51:55: #1 finished! INFO @ Wed, 08 Dec 2021 15:51:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:51:55: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:51:55: #2 number of paired peaks: 474 WARNING @ Wed, 08 Dec 2021 15:51:55: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Wed, 08 Dec 2021 15:51:55: start model_add_line... INFO @ Wed, 08 Dec 2021 15:51:55: start X-correlation... INFO @ Wed, 08 Dec 2021 15:51:55: end of X-cor INFO @ Wed, 08 Dec 2021 15:51:55: #2 finished! INFO @ Wed, 08 Dec 2021 15:51:55: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 15:51:55: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 15:51:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.05_model.r WARNING @ Wed, 08 Dec 2021 15:51:55: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:51:55: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 15:51:55: #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 15:51:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:51:56: 17000000 INFO @ Wed, 08 Dec 2021 15:52:04: 17000000 INFO @ Wed, 08 Dec 2021 15:52:08: 18000000 INFO @ Wed, 08 Dec 2021 15:52:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:52:18: 18000000 INFO @ Wed, 08 Dec 2021 15:52:21: 19000000 INFO @ Wed, 08 Dec 2021 15:52:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:52:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:52:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.05_summits.bed INFO @ Wed, 08 Dec 2021 15:52:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (530 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:52:32: 19000000 INFO @ Wed, 08 Dec 2021 15:52:34: 20000000 INFO @ Wed, 08 Dec 2021 15:52:40: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:52:40: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:52:40: #1 total tags in treatment: 6819765 INFO @ Wed, 08 Dec 2021 15:52:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:52:40: #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 15:52:41: #1 tags after filtering in treatment: 6401734 INFO @ Wed, 08 Dec 2021 15:52:41: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 15:52:41: #1 finished! INFO @ Wed, 08 Dec 2021 15:52:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:52:41: #2 number of paired peaks: 474 WARNING @ Wed, 08 Dec 2021 15:52:41: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Wed, 08 Dec 2021 15:52:41: start model_add_line... INFO @ Wed, 08 Dec 2021 15:52:41: start X-correlation... INFO @ Wed, 08 Dec 2021 15:52:41: end of X-cor INFO @ Wed, 08 Dec 2021 15:52:41: #2 finished! INFO @ Wed, 08 Dec 2021 15:52:41: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 15:52:41: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 15:52:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.20_model.r WARNING @ Wed, 08 Dec 2021 15:52:41: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:52:41: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 15:52:41: #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 15:52:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:52:46: 20000000 INFO @ Wed, 08 Dec 2021 15:52:54: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:52:54: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:52:54: #1 total tags in treatment: 6819765 INFO @ Wed, 08 Dec 2021 15:52:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:52:54: #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 15:52:54: #1 tags after filtering in treatment: 6401734 INFO @ Wed, 08 Dec 2021 15:52:54: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 15:52:54: #1 finished! INFO @ Wed, 08 Dec 2021 15:52:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:52:54: #2 number of paired peaks: 474 WARNING @ Wed, 08 Dec 2021 15:52:54: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Wed, 08 Dec 2021 15:52:54: start model_add_line... INFO @ Wed, 08 Dec 2021 15:52:54: start X-correlation... INFO @ Wed, 08 Dec 2021 15:52:54: end of X-cor INFO @ Wed, 08 Dec 2021 15:52:54: #2 finished! INFO @ Wed, 08 Dec 2021 15:52:54: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 15:52:54: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 15:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.10_model.r WARNING @ Wed, 08 Dec 2021 15:52:54: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:52:54: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 15:52:54: #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 15:52:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:53:02: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.20_summits.bed INFO @ Wed, 08 Dec 2021 15:53:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:53:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:53:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:53:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:53:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641207/SRX10641207.10_summits.bed INFO @ Wed, 08 Dec 2021 15:53:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (327 records, 4 fields): 2 millis CompletedMACS2peakCalling