Job ID = 6368847 SRX = SRX6619546 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:30:57 prefetch.2.10.7: 1) Downloading 'SRR9866063'... 2020-06-16T00:30:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:34 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:34 prefetch.2.10.7: 1) 'SRR9866063' was downloaded successfully 2020-06-16T00:35:34 prefetch.2.10.7: 'SRR9866063' has 0 unresolved dependencies Read 12089929 spots for SRR9866063/SRR9866063.sra Written 12089929 spots for SRR9866063/SRR9866063.sra 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: 00:22:21 12089929 reads; of these: 12089929 (100.00%) were paired; of these: 6233829 (51.56%) aligned concordantly 0 times 4826646 (39.92%) aligned concordantly exactly 1 time 1029454 (8.51%) aligned concordantly >1 times ---- 6233829 pairs aligned concordantly 0 times; of these: 3143117 (50.42%) aligned discordantly 1 time ---- 3090712 pairs aligned 0 times concordantly or discordantly; of these: 6181424 mates make up the pairs; of these: 5144743 (83.23%) aligned 0 times 390234 (6.31%) aligned exactly 1 time 646447 (10.46%) aligned >1 times 78.72% overall alignment rate Time searching: 00:22:21 Overall time: 00:22:21 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] 562984 / 8843790 = 0.0637 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 @ Tue, 16 Jun 2020 10:08:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.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 @ Tue, 16 Jun 2020 10:08:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:08:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:08:35: 1000000 INFO @ Tue, 16 Jun 2020 10:08:44: 2000000 INFO @ Tue, 16 Jun 2020 10:08:52: 3000000 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 @ Tue, 16 Jun 2020 10:08:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.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 @ Tue, 16 Jun 2020 10:08:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:08:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:01: 4000000 INFO @ Tue, 16 Jun 2020 10:09:06: 1000000 INFO @ Tue, 16 Jun 2020 10:09:11: 5000000 INFO @ Tue, 16 Jun 2020 10:09:15: 2000000 INFO @ Tue, 16 Jun 2020 10:09:20: 6000000 INFO @ Tue, 16 Jun 2020 10:09:24: 3000000 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 @ Tue, 16 Jun 2020 10:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.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 @ Tue, 16 Jun 2020 10:09:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:09:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:29: 7000000 INFO @ Tue, 16 Jun 2020 10:09:34: 4000000 INFO @ Tue, 16 Jun 2020 10:09:37: 1000000 INFO @ Tue, 16 Jun 2020 10:09:40: 8000000 INFO @ Tue, 16 Jun 2020 10:09:45: 5000000 INFO @ Tue, 16 Jun 2020 10:09:47: 2000000 INFO @ Tue, 16 Jun 2020 10:09:50: 9000000 INFO @ Tue, 16 Jun 2020 10:09:55: 6000000 INFO @ Tue, 16 Jun 2020 10:09:57: 3000000 INFO @ Tue, 16 Jun 2020 10:10:01: 10000000 INFO @ Tue, 16 Jun 2020 10:10:05: 7000000 INFO @ Tue, 16 Jun 2020 10:10:07: 4000000 INFO @ Tue, 16 Jun 2020 10:10:11: 11000000 INFO @ Tue, 16 Jun 2020 10:10:16: 8000000 INFO @ Tue, 16 Jun 2020 10:10:17: 5000000 INFO @ Tue, 16 Jun 2020 10:10:21: 12000000 INFO @ Tue, 16 Jun 2020 10:10:26: 9000000 INFO @ Tue, 16 Jun 2020 10:10:27: 6000000 INFO @ Tue, 16 Jun 2020 10:10:31: 13000000 INFO @ Tue, 16 Jun 2020 10:10:36: 10000000 INFO @ Tue, 16 Jun 2020 10:10:38: 7000000 INFO @ Tue, 16 Jun 2020 10:10:41: 14000000 INFO @ Tue, 16 Jun 2020 10:10:46: 11000000 INFO @ Tue, 16 Jun 2020 10:10:48: 8000000 INFO @ Tue, 16 Jun 2020 10:10:52: 15000000 INFO @ Tue, 16 Jun 2020 10:10:56: 12000000 INFO @ Tue, 16 Jun 2020 10:10:58: 9000000 INFO @ Tue, 16 Jun 2020 10:11:02: 16000000 INFO @ Tue, 16 Jun 2020 10:11:07: 13000000 INFO @ Tue, 16 Jun 2020 10:11:08: 10000000 INFO @ Tue, 16 Jun 2020 10:11:12: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:11:17: 14000000 INFO @ Tue, 16 Jun 2020 10:11:18: 11000000 INFO @ Tue, 16 Jun 2020 10:11:21: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:11:21: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:11:21: #1 total tags in treatment: 5462995 INFO @ Tue, 16 Jun 2020 10:11:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:11:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:11:21: #1 tags after filtering in treatment: 4950575 INFO @ Tue, 16 Jun 2020 10:11:21: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 10:11:21: #1 finished! INFO @ Tue, 16 Jun 2020 10:11:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:11:22: #2 number of paired peaks: 389 WARNING @ Tue, 16 Jun 2020 10:11:22: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Tue, 16 Jun 2020 10:11:22: start model_add_line... INFO @ Tue, 16 Jun 2020 10:11:22: start X-correlation... INFO @ Tue, 16 Jun 2020 10:11:22: end of X-cor INFO @ Tue, 16 Jun 2020 10:11:22: #2 finished! INFO @ Tue, 16 Jun 2020 10:11:22: #2 predicted fragment length is 214 bps INFO @ Tue, 16 Jun 2020 10:11:22: #2 alternative fragment length(s) may be 214,230 bps INFO @ Tue, 16 Jun 2020 10:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.05_model.r WARNING @ Tue, 16 Jun 2020 10:11:22: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:11:22: #2 You may need to consider one of the other alternative d(s): 214,230 WARNING @ Tue, 16 Jun 2020 10:11:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:11:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:11:27: 15000000 INFO @ Tue, 16 Jun 2020 10:11:28: 12000000 INFO @ Tue, 16 Jun 2020 10:11:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:11:37: 16000000 INFO @ Tue, 16 Jun 2020 10:11:38: 13000000 INFO @ Tue, 16 Jun 2020 10:11:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:11:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:11:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.05_summits.bed INFO @ Tue, 16 Jun 2020 10:11:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (363 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:11:47: 17000000 INFO @ Tue, 16 Jun 2020 10:11:48: 14000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:11:56: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:11:56: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:11:56: #1 total tags in treatment: 5462995 INFO @ Tue, 16 Jun 2020 10:11:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:11:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:11:56: #1 tags after filtering in treatment: 4950575 INFO @ Tue, 16 Jun 2020 10:11:56: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 10:11:56: #1 finished! INFO @ Tue, 16 Jun 2020 10:11:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:11:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:11:56: #2 number of paired peaks: 389 WARNING @ Tue, 16 Jun 2020 10:11:56: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Tue, 16 Jun 2020 10:11:56: start model_add_line... INFO @ Tue, 16 Jun 2020 10:11:57: start X-correlation... INFO @ Tue, 16 Jun 2020 10:11:57: end of X-cor INFO @ Tue, 16 Jun 2020 10:11:57: #2 finished! INFO @ Tue, 16 Jun 2020 10:11:57: #2 predicted fragment length is 214 bps INFO @ Tue, 16 Jun 2020 10:11:57: #2 alternative fragment length(s) may be 214,230 bps INFO @ Tue, 16 Jun 2020 10:11:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.10_model.r WARNING @ Tue, 16 Jun 2020 10:11:57: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:11:57: #2 You may need to consider one of the other alternative d(s): 214,230 WARNING @ Tue, 16 Jun 2020 10:11:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:11:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:11:58: 15000000 INFO @ Tue, 16 Jun 2020 10:12:07: 16000000 INFO @ Tue, 16 Jun 2020 10:12:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.10_summits.bed INFO @ Tue, 16 Jun 2020 10:12:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (248 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:12:16: 17000000 INFO @ Tue, 16 Jun 2020 10:12:23: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:12:23: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:12:23: #1 total tags in treatment: 5462995 INFO @ Tue, 16 Jun 2020 10:12:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:12:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:12:23: #1 tags after filtering in treatment: 4950575 INFO @ Tue, 16 Jun 2020 10:12:23: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 10:12:23: #1 finished! INFO @ Tue, 16 Jun 2020 10:12:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:12:24: #2 number of paired peaks: 389 WARNING @ Tue, 16 Jun 2020 10:12:24: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Tue, 16 Jun 2020 10:12:24: start model_add_line... INFO @ Tue, 16 Jun 2020 10:12:24: start X-correlation... INFO @ Tue, 16 Jun 2020 10:12:24: end of X-cor INFO @ Tue, 16 Jun 2020 10:12:24: #2 finished! INFO @ Tue, 16 Jun 2020 10:12:24: #2 predicted fragment length is 214 bps INFO @ Tue, 16 Jun 2020 10:12:24: #2 alternative fragment length(s) may be 214,230 bps INFO @ Tue, 16 Jun 2020 10:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.20_model.r WARNING @ Tue, 16 Jun 2020 10:12:24: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:12:24: #2 You may need to consider one of the other alternative d(s): 214,230 WARNING @ Tue, 16 Jun 2020 10:12:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:12:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:12:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619546/SRX6619546.20_summits.bed INFO @ Tue, 16 Jun 2020 10:12:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 1 millis CompletedMACS2peakCalling