Job ID = 6367237 SRX = SRX3058057 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:27:06 prefetch.2.10.7: 1) Downloading 'SRR5892348'... 2020-06-15T23:27:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:33 prefetch.2.10.7: 1) 'SRR5892348' was downloaded successfully 2020-06-15T23:44:33 prefetch.2.10.7: 'SRR5892348' has 0 unresolved dependencies Read 26026647 spots for SRR5892348/SRR5892348.sra Written 26026647 spots for SRR5892348/SRR5892348.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: 00:51:51 26026647 reads; of these: 26026647 (100.00%) were paired; of these: 3131493 (12.03%) aligned concordantly 0 times 19787660 (76.03%) aligned concordantly exactly 1 time 3107494 (11.94%) aligned concordantly >1 times ---- 3131493 pairs aligned concordantly 0 times; of these: 557738 (17.81%) aligned discordantly 1 time ---- 2573755 pairs aligned 0 times concordantly or discordantly; of these: 5147510 mates make up the pairs; of these: 4563005 (88.64%) aligned 0 times 380634 (7.39%) aligned exactly 1 time 203871 (3.96%) aligned >1 times 91.23% overall alignment rate Time searching: 00:51:51 Overall time: 00:51:51 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 36 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] 8784231 / 23365534 = 0.3759 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 10:05:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.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 10:05:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:05:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:05:40: 1000000 INFO @ Tue, 16 Jun 2020 10:05:49: 2000000 INFO @ Tue, 16 Jun 2020 10:05:57: 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 10:06:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.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 10:06:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:06:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:06:05: 4000000 INFO @ Tue, 16 Jun 2020 10:06:11: 1000000 INFO @ Tue, 16 Jun 2020 10:06:14: 5000000 INFO @ Tue, 16 Jun 2020 10:06:20: 2000000 INFO @ Tue, 16 Jun 2020 10:06:23: 6000000 INFO @ Tue, 16 Jun 2020 10:06:29: 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 10:06:32: 7000000 INFO @ Tue, 16 Jun 2020 10:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.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 10:06:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:06:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:06:38: 4000000 INFO @ Tue, 16 Jun 2020 10:06:41: 8000000 INFO @ Tue, 16 Jun 2020 10:06:42: 1000000 INFO @ Tue, 16 Jun 2020 10:06:47: 5000000 INFO @ Tue, 16 Jun 2020 10:06:50: 9000000 INFO @ Tue, 16 Jun 2020 10:06:51: 2000000 INFO @ Tue, 16 Jun 2020 10:06:55: 6000000 INFO @ Tue, 16 Jun 2020 10:06:59: 10000000 INFO @ Tue, 16 Jun 2020 10:07:00: 3000000 INFO @ Tue, 16 Jun 2020 10:07:04: 7000000 INFO @ Tue, 16 Jun 2020 10:07:07: 11000000 INFO @ Tue, 16 Jun 2020 10:07:09: 4000000 INFO @ Tue, 16 Jun 2020 10:07:12: 8000000 INFO @ Tue, 16 Jun 2020 10:07:16: 12000000 INFO @ Tue, 16 Jun 2020 10:07:18: 5000000 INFO @ Tue, 16 Jun 2020 10:07:21: 9000000 INFO @ Tue, 16 Jun 2020 10:07:24: 13000000 INFO @ Tue, 16 Jun 2020 10:07:26: 6000000 INFO @ Tue, 16 Jun 2020 10:07:29: 10000000 INFO @ Tue, 16 Jun 2020 10:07:33: 14000000 INFO @ Tue, 16 Jun 2020 10:07:35: 7000000 INFO @ Tue, 16 Jun 2020 10:07:38: 11000000 INFO @ Tue, 16 Jun 2020 10:07:41: 15000000 INFO @ Tue, 16 Jun 2020 10:07:43: 8000000 INFO @ Tue, 16 Jun 2020 10:07:46: 12000000 INFO @ Tue, 16 Jun 2020 10:07:49: 16000000 INFO @ Tue, 16 Jun 2020 10:07:51: 9000000 INFO @ Tue, 16 Jun 2020 10:07:54: 13000000 INFO @ Tue, 16 Jun 2020 10:07:58: 17000000 INFO @ Tue, 16 Jun 2020 10:08:00: 10000000 INFO @ Tue, 16 Jun 2020 10:08:03: 14000000 INFO @ Tue, 16 Jun 2020 10:08:06: 18000000 INFO @ Tue, 16 Jun 2020 10:08:08: 11000000 INFO @ Tue, 16 Jun 2020 10:08:11: 15000000 INFO @ Tue, 16 Jun 2020 10:08:14: 19000000 INFO @ Tue, 16 Jun 2020 10:08:16: 12000000 INFO @ Tue, 16 Jun 2020 10:08:19: 16000000 INFO @ Tue, 16 Jun 2020 10:08:22: 20000000 INFO @ Tue, 16 Jun 2020 10:08:25: 13000000 INFO @ Tue, 16 Jun 2020 10:08:27: 17000000 INFO @ Tue, 16 Jun 2020 10:08:30: 21000000 INFO @ Tue, 16 Jun 2020 10:08:33: 14000000 INFO @ Tue, 16 Jun 2020 10:08:35: 18000000 INFO @ Tue, 16 Jun 2020 10:08:38: 22000000 INFO @ Tue, 16 Jun 2020 10:08:41: 15000000 INFO @ Tue, 16 Jun 2020 10:08:44: 19000000 INFO @ Tue, 16 Jun 2020 10:08:46: 23000000 INFO @ Tue, 16 Jun 2020 10:08:49: 16000000 INFO @ Tue, 16 Jun 2020 10:08:52: 20000000 INFO @ Tue, 16 Jun 2020 10:08:55: 24000000 INFO @ Tue, 16 Jun 2020 10:08:58: 17000000 INFO @ Tue, 16 Jun 2020 10:09:00: 21000000 INFO @ Tue, 16 Jun 2020 10:09:03: 25000000 INFO @ Tue, 16 Jun 2020 10:09:06: 18000000 INFO @ Tue, 16 Jun 2020 10:09:08: 22000000 INFO @ Tue, 16 Jun 2020 10:09:11: 26000000 INFO @ Tue, 16 Jun 2020 10:09:14: 19000000 INFO @ Tue, 16 Jun 2020 10:09:16: 23000000 INFO @ Tue, 16 Jun 2020 10:09:19: 27000000 INFO @ Tue, 16 Jun 2020 10:09:22: 20000000 INFO @ Tue, 16 Jun 2020 10:09:24: 24000000 INFO @ Tue, 16 Jun 2020 10:09:27: 28000000 INFO @ Tue, 16 Jun 2020 10:09:30: 21000000 INFO @ Tue, 16 Jun 2020 10:09:32: 25000000 INFO @ Tue, 16 Jun 2020 10:09:36: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:09:38: 22000000 INFO @ Tue, 16 Jun 2020 10:09:40: 26000000 INFO @ Tue, 16 Jun 2020 10:09:43: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:09:43: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:09:43: #1 total tags in treatment: 14254547 INFO @ Tue, 16 Jun 2020 10:09:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:09:43: #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 10:09:44: #1 tags after filtering in treatment: 12680284 INFO @ Tue, 16 Jun 2020 10:09:44: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 10:09:44: #1 finished! INFO @ Tue, 16 Jun 2020 10:09:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:09:44: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 10:09:44: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 10:09:44: start model_add_line... INFO @ Tue, 16 Jun 2020 10:09:45: start X-correlation... INFO @ Tue, 16 Jun 2020 10:09:45: end of X-cor INFO @ Tue, 16 Jun 2020 10:09:45: #2 finished! INFO @ Tue, 16 Jun 2020 10:09:45: #2 predicted fragment length is 217 bps INFO @ Tue, 16 Jun 2020 10:09:45: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 16 Jun 2020 10:09:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.05_model.r WARNING @ Tue, 16 Jun 2020 10:09:45: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:09:45: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 16 Jun 2020 10:09:45: #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 10:09:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:09:47: 23000000 INFO @ Tue, 16 Jun 2020 10:09:48: 27000000 INFO @ Tue, 16 Jun 2020 10:09:55: 24000000 INFO @ Tue, 16 Jun 2020 10:09:57: 28000000 INFO @ Tue, 16 Jun 2020 10:10:03: 25000000 INFO @ Tue, 16 Jun 2020 10:10:05: 29000000 INFO @ Tue, 16 Jun 2020 10:10:11: 26000000 INFO @ Tue, 16 Jun 2020 10:10:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:10:12: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:10:12: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:10:12: #1 total tags in treatment: 14254547 INFO @ Tue, 16 Jun 2020 10:10:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:10:12: #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 10:10:13: #1 tags after filtering in treatment: 12680284 INFO @ Tue, 16 Jun 2020 10:10:13: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 10:10:13: #1 finished! INFO @ Tue, 16 Jun 2020 10:10:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:10:13: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 10:10:13: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 10:10:13: start model_add_line... INFO @ Tue, 16 Jun 2020 10:10:14: start X-correlation... INFO @ Tue, 16 Jun 2020 10:10:14: end of X-cor INFO @ Tue, 16 Jun 2020 10:10:14: #2 finished! INFO @ Tue, 16 Jun 2020 10:10:14: #2 predicted fragment length is 217 bps INFO @ Tue, 16 Jun 2020 10:10:14: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 16 Jun 2020 10:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.10_model.r WARNING @ Tue, 16 Jun 2020 10:10:14: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:10:14: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 16 Jun 2020 10:10:14: #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 10:10:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:10:19: 27000000 INFO @ Tue, 16 Jun 2020 10:10:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:10:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:10:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.05_summits.bed INFO @ Tue, 16 Jun 2020 10:10:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4030 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:10:26: 28000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:10:34: 29000000 INFO @ Tue, 16 Jun 2020 10:10:41: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:10:41: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:10:41: #1 total tags in treatment: 14254547 INFO @ Tue, 16 Jun 2020 10:10:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:10:41: #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 10:10:42: #1 tags after filtering in treatment: 12680284 INFO @ Tue, 16 Jun 2020 10:10:42: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 10:10:42: #1 finished! INFO @ Tue, 16 Jun 2020 10:10:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:10:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:10:43: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 10:10:43: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 10:10:43: start model_add_line... INFO @ Tue, 16 Jun 2020 10:10:43: start X-correlation... INFO @ Tue, 16 Jun 2020 10:10:43: end of X-cor INFO @ Tue, 16 Jun 2020 10:10:43: #2 finished! INFO @ Tue, 16 Jun 2020 10:10:43: #2 predicted fragment length is 217 bps INFO @ Tue, 16 Jun 2020 10:10:43: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 16 Jun 2020 10:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.20_model.r WARNING @ Tue, 16 Jun 2020 10:10:43: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:10:43: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 16 Jun 2020 10:10:43: #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 10:10:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:10:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:10:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:10:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.10_summits.bed INFO @ Tue, 16 Jun 2020 10:10:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2851 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:11:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3058057/SRX3058057.20_summits.bed INFO @ Tue, 16 Jun 2020 10:11:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1793 records, 4 fields): 4 millis CompletedMACS2peakCalling