Job ID = 6367820 SRX = SRX4085388 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:34:50 prefetch.2.10.7: 1) Downloading 'SRR7167417'... 2020-06-15T23:34:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:25 prefetch.2.10.7: 1) 'SRR7167417' was downloaded successfully Read 14999107 spots for SRR7167417/SRR7167417.sra Written 14999107 spots for SRR7167417/SRR7167417.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: 00:09:41 14999107 reads; of these: 14999107 (100.00%) were paired; of these: 5359810 (35.73%) aligned concordantly 0 times 8474024 (56.50%) aligned concordantly exactly 1 time 1165273 (7.77%) aligned concordantly >1 times ---- 5359810 pairs aligned concordantly 0 times; of these: 248200 (4.63%) aligned discordantly 1 time ---- 5111610 pairs aligned 0 times concordantly or discordantly; of these: 10223220 mates make up the pairs; of these: 7256617 (70.98%) aligned 0 times 2606081 (25.49%) aligned exactly 1 time 360522 (3.53%) aligned >1 times 75.81% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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] 587121 / 9776838 = 0.0601 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 08:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.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 08:58:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:27: 1000000 INFO @ Tue, 16 Jun 2020 08:58:33: 2000000 INFO @ Tue, 16 Jun 2020 08:58:39: 3000000 INFO @ Tue, 16 Jun 2020 08:58:45: 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 @ Tue, 16 Jun 2020 08:58:51: 5000000 INFO @ Tue, 16 Jun 2020 08:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.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 08:58:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:58: 6000000 INFO @ Tue, 16 Jun 2020 08:58:58: 1000000 INFO @ Tue, 16 Jun 2020 08:59:05: 2000000 INFO @ Tue, 16 Jun 2020 08:59:05: 7000000 INFO @ Tue, 16 Jun 2020 08:59:11: 8000000 INFO @ Tue, 16 Jun 2020 08:59:11: 3000000 INFO @ Tue, 16 Jun 2020 08:59:17: 9000000 INFO @ Tue, 16 Jun 2020 08:59:18: 4000000 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 08:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.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 08:59:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:24: 10000000 INFO @ Tue, 16 Jun 2020 08:59:24: 5000000 INFO @ Tue, 16 Jun 2020 08:59:28: 1000000 INFO @ Tue, 16 Jun 2020 08:59:31: 11000000 INFO @ Tue, 16 Jun 2020 08:59:31: 6000000 INFO @ Tue, 16 Jun 2020 08:59:36: 2000000 INFO @ Tue, 16 Jun 2020 08:59:37: 12000000 INFO @ Tue, 16 Jun 2020 08:59:37: 7000000 INFO @ Tue, 16 Jun 2020 08:59:43: 3000000 INFO @ Tue, 16 Jun 2020 08:59:44: 13000000 INFO @ Tue, 16 Jun 2020 08:59:44: 8000000 INFO @ Tue, 16 Jun 2020 08:59:50: 4000000 INFO @ Tue, 16 Jun 2020 08:59:51: 14000000 INFO @ Tue, 16 Jun 2020 08:59:51: 9000000 INFO @ Tue, 16 Jun 2020 08:59:57: 5000000 INFO @ Tue, 16 Jun 2020 08:59:57: 15000000 INFO @ Tue, 16 Jun 2020 08:59:57: 10000000 INFO @ Tue, 16 Jun 2020 09:00:04: 6000000 INFO @ Tue, 16 Jun 2020 09:00:04: 16000000 INFO @ Tue, 16 Jun 2020 09:00:04: 11000000 INFO @ Tue, 16 Jun 2020 09:00:11: 7000000 INFO @ Tue, 16 Jun 2020 09:00:11: 17000000 INFO @ Tue, 16 Jun 2020 09:00:11: 12000000 INFO @ Tue, 16 Jun 2020 09:00:18: 13000000 INFO @ Tue, 16 Jun 2020 09:00:18: 18000000 INFO @ Tue, 16 Jun 2020 09:00:18: 8000000 INFO @ Tue, 16 Jun 2020 09:00:24: 14000000 INFO @ Tue, 16 Jun 2020 09:00:24: 19000000 INFO @ Tue, 16 Jun 2020 09:00:25: 9000000 INFO @ Tue, 16 Jun 2020 09:00:31: 20000000 INFO @ Tue, 16 Jun 2020 09:00:31: 15000000 INFO @ Tue, 16 Jun 2020 09:00:32: 10000000 INFO @ Tue, 16 Jun 2020 09:00:38: 16000000 INFO @ Tue, 16 Jun 2020 09:00:38: 21000000 INFO @ Tue, 16 Jun 2020 09:00:39: 11000000 INFO @ Tue, 16 Jun 2020 09:00:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:00:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:00:42: #1 total tags in treatment: 9059775 INFO @ Tue, 16 Jun 2020 09:00:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:42: #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 09:00:42: #1 tags after filtering in treatment: 8117644 INFO @ Tue, 16 Jun 2020 09:00:42: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:00:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:43: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 09:00:43: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:43: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 09:00:43: #2 alternative fragment length(s) may be 4,95,214 bps INFO @ Tue, 16 Jun 2020 09:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.05_model.r WARNING @ Tue, 16 Jun 2020 09:00:43: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:43: #2 You may need to consider one of the other alternative d(s): 4,95,214 WARNING @ Tue, 16 Jun 2020 09:00:43: #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 09:00:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:44: 17000000 INFO @ Tue, 16 Jun 2020 09:00:46: 12000000 INFO @ Tue, 16 Jun 2020 09:00:51: 18000000 INFO @ Tue, 16 Jun 2020 09:00:53: 13000000 INFO @ Tue, 16 Jun 2020 09:00:58: 19000000 INFO @ Tue, 16 Jun 2020 09:01:00: 14000000 INFO @ Tue, 16 Jun 2020 09:01:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:04: 20000000 INFO @ Tue, 16 Jun 2020 09:01:07: 15000000 INFO @ Tue, 16 Jun 2020 09:01:11: 21000000 INFO @ Tue, 16 Jun 2020 09:01:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.05_summits.bed INFO @ Tue, 16 Jun 2020 09:01:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1075 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:14: 16000000 INFO @ Tue, 16 Jun 2020 09:01:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:01:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:01:15: #1 total tags in treatment: 9059775 INFO @ Tue, 16 Jun 2020 09:01:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:15: #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 09:01:15: #1 tags after filtering in treatment: 8117644 INFO @ Tue, 16 Jun 2020 09:01:15: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:01:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:15: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 09:01:15: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 09:01:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:16: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 09:01:16: #2 alternative fragment length(s) may be 4,95,214 bps INFO @ Tue, 16 Jun 2020 09:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.10_model.r WARNING @ Tue, 16 Jun 2020 09:01:16: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:01:16: #2 You may need to consider one of the other alternative d(s): 4,95,214 WARNING @ Tue, 16 Jun 2020 09:01:16: #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 09:01:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:21: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:01:27: 18000000 INFO @ Tue, 16 Jun 2020 09:01:34: 19000000 INFO @ Tue, 16 Jun 2020 09:01:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:40: 20000000 INFO @ Tue, 16 Jun 2020 09:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.10_summits.bed INFO @ Tue, 16 Jun 2020 09:01:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:47: 21000000 INFO @ Tue, 16 Jun 2020 09:01:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:01:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:01:50: #1 total tags in treatment: 9059775 INFO @ Tue, 16 Jun 2020 09:01:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:50: #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 09:01:50: #1 tags after filtering in treatment: 8117644 INFO @ Tue, 16 Jun 2020 09:01:50: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:01:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:51: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 09:01:51: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 09:01:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:51: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 09:01:51: #2 alternative fragment length(s) may be 4,95,214 bps INFO @ Tue, 16 Jun 2020 09:01:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.20_model.r WARNING @ Tue, 16 Jun 2020 09:01:51: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:01:51: #2 You may need to consider one of the other alternative d(s): 4,95,214 WARNING @ Tue, 16 Jun 2020 09:01:51: #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 09:01:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085388/SRX4085388.20_summits.bed INFO @ Tue, 16 Jun 2020 09:02:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (112 records, 4 fields): 1 millis CompletedMACS2peakCalling