Job ID = 6367808 SRX = SRX4085376 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:46:29 prefetch.2.10.7: 1) Downloading 'SRR7167405'... 2020-06-15T23:46:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:30 prefetch.2.10.7: 1) 'SRR7167405' was downloaded successfully Read 17630602 spots for SRR7167405/SRR7167405.sra Written 17630602 spots for SRR7167405/SRR7167405.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: 00:11:03 17630602 reads; of these: 17630602 (100.00%) were paired; of these: 9436425 (53.52%) aligned concordantly 0 times 6977911 (39.58%) aligned concordantly exactly 1 time 1216266 (6.90%) aligned concordantly >1 times ---- 9436425 pairs aligned concordantly 0 times; of these: 475199 (5.04%) aligned discordantly 1 time ---- 8961226 pairs aligned 0 times concordantly or discordantly; of these: 17922452 mates make up the pairs; of these: 12998922 (72.53%) aligned 0 times 4330119 (24.16%) aligned exactly 1 time 593411 (3.31%) aligned >1 times 63.14% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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] 553782 / 8513024 = 0.0651 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 09:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.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 09:12:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:21: 1000000 INFO @ Tue, 16 Jun 2020 09:12:27: 2000000 INFO @ Tue, 16 Jun 2020 09:12:33: 3000000 INFO @ Tue, 16 Jun 2020 09:12:39: 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 09:12:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.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 09:12:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:46: 5000000 INFO @ Tue, 16 Jun 2020 09:12:51: 1000000 INFO @ Tue, 16 Jun 2020 09:12:52: 6000000 INFO @ Tue, 16 Jun 2020 09:12:57: 2000000 INFO @ Tue, 16 Jun 2020 09:12:58: 7000000 INFO @ Tue, 16 Jun 2020 09:13:03: 3000000 INFO @ Tue, 16 Jun 2020 09:13:05: 8000000 INFO @ Tue, 16 Jun 2020 09:13:09: 4000000 INFO @ Tue, 16 Jun 2020 09:13:11: 9000000 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 09:13:15: 5000000 INFO @ Tue, 16 Jun 2020 09:13:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.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 09:13:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:18: 10000000 INFO @ Tue, 16 Jun 2020 09:13:21: 6000000 INFO @ Tue, 16 Jun 2020 09:13:21: 1000000 INFO @ Tue, 16 Jun 2020 09:13:24: 11000000 INFO @ Tue, 16 Jun 2020 09:13:28: 2000000 INFO @ Tue, 16 Jun 2020 09:13:28: 7000000 INFO @ Tue, 16 Jun 2020 09:13:30: 12000000 INFO @ Tue, 16 Jun 2020 09:13:34: 3000000 INFO @ Tue, 16 Jun 2020 09:13:34: 8000000 INFO @ Tue, 16 Jun 2020 09:13:37: 13000000 INFO @ Tue, 16 Jun 2020 09:13:40: 9000000 INFO @ Tue, 16 Jun 2020 09:13:40: 4000000 INFO @ Tue, 16 Jun 2020 09:13:44: 14000000 INFO @ Tue, 16 Jun 2020 09:13:46: 10000000 INFO @ Tue, 16 Jun 2020 09:13:46: 5000000 INFO @ Tue, 16 Jun 2020 09:13:50: 15000000 INFO @ Tue, 16 Jun 2020 09:13:53: 11000000 INFO @ Tue, 16 Jun 2020 09:13:53: 6000000 INFO @ Tue, 16 Jun 2020 09:13:56: 16000000 INFO @ Tue, 16 Jun 2020 09:13:59: 12000000 INFO @ Tue, 16 Jun 2020 09:13:59: 7000000 INFO @ Tue, 16 Jun 2020 09:14:03: 17000000 INFO @ Tue, 16 Jun 2020 09:14:05: 13000000 INFO @ Tue, 16 Jun 2020 09:14:06: 8000000 INFO @ Tue, 16 Jun 2020 09:14:09: 18000000 INFO @ Tue, 16 Jun 2020 09:14:11: 14000000 INFO @ Tue, 16 Jun 2020 09:14:12: 9000000 INFO @ Tue, 16 Jun 2020 09:14:16: 19000000 INFO @ Tue, 16 Jun 2020 09:14:18: 15000000 INFO @ Tue, 16 Jun 2020 09:14:19: 10000000 INFO @ Tue, 16 Jun 2020 09:14:22: 20000000 INFO @ Tue, 16 Jun 2020 09:14:24: 16000000 INFO @ Tue, 16 Jun 2020 09:14:25: 11000000 INFO @ Tue, 16 Jun 2020 09:14:29: 21000000 INFO @ Tue, 16 Jun 2020 09:14:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:14:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:14:30: #1 total tags in treatment: 7661253 INFO @ Tue, 16 Jun 2020 09:14:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:30: #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 09:14:30: #1 tags after filtering in treatment: 6726172 INFO @ Tue, 16 Jun 2020 09:14:30: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:14:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:30: #2 number of paired peaks: 511 WARNING @ Tue, 16 Jun 2020 09:14:30: Fewer paired peaks (511) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 511 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:30: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 09:14:30: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 16 Jun 2020 09:14:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.05_model.r WARNING @ Tue, 16 Jun 2020 09:14:30: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:14:30: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 16 Jun 2020 09:14:30: #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 09:14:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:31: 17000000 INFO @ Tue, 16 Jun 2020 09:14:32: 12000000 INFO @ Tue, 16 Jun 2020 09:14:37: 18000000 INFO @ Tue, 16 Jun 2020 09:14:39: 13000000 INFO @ Tue, 16 Jun 2020 09:14:43: 19000000 INFO @ Tue, 16 Jun 2020 09:14:45: 14000000 INFO @ Tue, 16 Jun 2020 09:14:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:49: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:14:52: 15000000 INFO @ Tue, 16 Jun 2020 09:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.05_summits.bed INFO @ Tue, 16 Jun 2020 09:14:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3356 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:55: 21000000 INFO @ Tue, 16 Jun 2020 09:14:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:14:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:14:56: #1 total tags in treatment: 7661253 INFO @ Tue, 16 Jun 2020 09:14:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:56: #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 09:14:56: #1 tags after filtering in treatment: 6726172 INFO @ Tue, 16 Jun 2020 09:14:56: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:14:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:57: #2 number of paired peaks: 511 WARNING @ Tue, 16 Jun 2020 09:14:57: Fewer paired peaks (511) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 511 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:57: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 09:14:57: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 16 Jun 2020 09:14:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.10_model.r WARNING @ Tue, 16 Jun 2020 09:14:57: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:14:57: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 16 Jun 2020 09:14:57: #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 09:14:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:58: 16000000 INFO @ Tue, 16 Jun 2020 09:15:04: 17000000 INFO @ Tue, 16 Jun 2020 09:15:11: 18000000 INFO @ Tue, 16 Jun 2020 09:15:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:17: 19000000 INFO @ Tue, 16 Jun 2020 09:15:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.10_summits.bed INFO @ Tue, 16 Jun 2020 09:15:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1918 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:23: 20000000 INFO @ Tue, 16 Jun 2020 09:15:29: 21000000 INFO @ Tue, 16 Jun 2020 09:15:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:15:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:15:30: #1 total tags in treatment: 7661253 INFO @ Tue, 16 Jun 2020 09:15:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:30: #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 09:15:30: #1 tags after filtering in treatment: 6726172 INFO @ Tue, 16 Jun 2020 09:15:30: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:15:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:30: #2 number of paired peaks: 511 WARNING @ Tue, 16 Jun 2020 09:15:30: Fewer paired peaks (511) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 511 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:30: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 09:15:30: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 16 Jun 2020 09:15:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.20_model.r WARNING @ Tue, 16 Jun 2020 09:15:30: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:15:30: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 16 Jun 2020 09:15:30: #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 09:15:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:15:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085376/SRX4085376.20_summits.bed INFO @ Tue, 16 Jun 2020 09:15:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (906 records, 4 fields): 4 millis CompletedMACS2peakCalling