Job ID = 6367241 SRX = SRX3058060 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:19:31 prefetch.2.10.7: 1) Downloading 'SRR5892351'... 2020-06-15T23:19:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:35 prefetch.2.10.7: 1) 'SRR5892351' was downloaded successfully 2020-06-15T23:23:35 prefetch.2.10.7: 'SRR5892351' has 0 unresolved dependencies Read 15591285 spots for SRR5892351/SRR5892351.sra Written 15591285 spots for SRR5892351/SRR5892351.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: 00:29:47 15591285 reads; of these: 15591285 (100.00%) were paired; of these: 1531609 (9.82%) aligned concordantly 0 times 12364950 (79.31%) aligned concordantly exactly 1 time 1694726 (10.87%) aligned concordantly >1 times ---- 1531609 pairs aligned concordantly 0 times; of these: 127777 (8.34%) aligned discordantly 1 time ---- 1403832 pairs aligned 0 times concordantly or discordantly; of these: 2807664 mates make up the pairs; of these: 2598097 (92.54%) aligned 0 times 142143 (5.06%) aligned exactly 1 time 67424 (2.40%) aligned >1 times 91.67% overall alignment rate Time searching: 00:29:47 Overall time: 00:29:47 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 24 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] 2175243 / 14167368 = 0.1535 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 09:09:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.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 09:09:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:32: 1000000 INFO @ Tue, 16 Jun 2020 09:09:39: 2000000 INFO @ Tue, 16 Jun 2020 09:09:46: 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 09:09:53: 4000000 INFO @ Tue, 16 Jun 2020 09:09:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.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 09:09:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:00: 5000000 INFO @ Tue, 16 Jun 2020 09:10:03: 1000000 INFO @ Tue, 16 Jun 2020 09:10:07: 6000000 INFO @ Tue, 16 Jun 2020 09:10:10: 2000000 INFO @ Tue, 16 Jun 2020 09:10:15: 7000000 INFO @ Tue, 16 Jun 2020 09:10:17: 3000000 INFO @ Tue, 16 Jun 2020 09:10:22: 8000000 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 09:10:24: 4000000 INFO @ Tue, 16 Jun 2020 09:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.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 09:10:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:29: 9000000 INFO @ Tue, 16 Jun 2020 09:10:32: 5000000 INFO @ Tue, 16 Jun 2020 09:10:33: 1000000 INFO @ Tue, 16 Jun 2020 09:10:37: 10000000 INFO @ Tue, 16 Jun 2020 09:10:39: 6000000 INFO @ Tue, 16 Jun 2020 09:10:40: 2000000 INFO @ Tue, 16 Jun 2020 09:10:44: 11000000 INFO @ Tue, 16 Jun 2020 09:10:46: 7000000 INFO @ Tue, 16 Jun 2020 09:10:48: 3000000 INFO @ Tue, 16 Jun 2020 09:10:51: 12000000 INFO @ Tue, 16 Jun 2020 09:10:54: 8000000 INFO @ Tue, 16 Jun 2020 09:10:55: 4000000 INFO @ Tue, 16 Jun 2020 09:10:59: 13000000 INFO @ Tue, 16 Jun 2020 09:11:01: 9000000 INFO @ Tue, 16 Jun 2020 09:11:03: 5000000 INFO @ Tue, 16 Jun 2020 09:11:06: 14000000 INFO @ Tue, 16 Jun 2020 09:11:09: 10000000 INFO @ Tue, 16 Jun 2020 09:11:11: 6000000 INFO @ Tue, 16 Jun 2020 09:11:14: 15000000 INFO @ Tue, 16 Jun 2020 09:11:17: 11000000 INFO @ Tue, 16 Jun 2020 09:11:19: 7000000 INFO @ Tue, 16 Jun 2020 09:11:22: 16000000 INFO @ Tue, 16 Jun 2020 09:11:24: 12000000 INFO @ Tue, 16 Jun 2020 09:11:26: 8000000 INFO @ Tue, 16 Jun 2020 09:11:29: 17000000 INFO @ Tue, 16 Jun 2020 09:11:32: 13000000 INFO @ Tue, 16 Jun 2020 09:11:34: 9000000 INFO @ Tue, 16 Jun 2020 09:11:37: 18000000 INFO @ Tue, 16 Jun 2020 09:11:39: 14000000 INFO @ Tue, 16 Jun 2020 09:11:42: 10000000 INFO @ Tue, 16 Jun 2020 09:11:45: 19000000 INFO @ Tue, 16 Jun 2020 09:11:47: 15000000 INFO @ Tue, 16 Jun 2020 09:11:49: 11000000 INFO @ Tue, 16 Jun 2020 09:11:53: 20000000 INFO @ Tue, 16 Jun 2020 09:11:55: 16000000 INFO @ Tue, 16 Jun 2020 09:11:57: 12000000 INFO @ Tue, 16 Jun 2020 09:12:00: 21000000 INFO @ Tue, 16 Jun 2020 09:12:02: 17000000 INFO @ Tue, 16 Jun 2020 09:12:05: 13000000 INFO @ Tue, 16 Jun 2020 09:12:08: 22000000 INFO @ Tue, 16 Jun 2020 09:12:10: 18000000 INFO @ Tue, 16 Jun 2020 09:12:12: 14000000 INFO @ Tue, 16 Jun 2020 09:12:15: 23000000 INFO @ Tue, 16 Jun 2020 09:12:17: 19000000 INFO @ Tue, 16 Jun 2020 09:12:20: 15000000 INFO @ Tue, 16 Jun 2020 09:12:23: 24000000 INFO @ Tue, 16 Jun 2020 09:12:25: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 09:12:25: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 09:12:25: #1 total tags in treatment: 11898501 INFO @ Tue, 16 Jun 2020 09:12:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:25: #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 09:12:25: 20000000 INFO @ Tue, 16 Jun 2020 09:12:25: #1 tags after filtering in treatment: 11061583 INFO @ Tue, 16 Jun 2020 09:12:25: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 09:12:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:26: #2 number of paired peaks: 319 WARNING @ Tue, 16 Jun 2020 09:12:26: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:26: #2 predicted fragment length is 214 bps INFO @ Tue, 16 Jun 2020 09:12:26: #2 alternative fragment length(s) may be 214 bps INFO @ Tue, 16 Jun 2020 09:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.05_model.r WARNING @ Tue, 16 Jun 2020 09:12:26: #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 09:12:26: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Tue, 16 Jun 2020 09:12:26: #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 09:12:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:28: 16000000 INFO @ Tue, 16 Jun 2020 09:12:33: 21000000 INFO @ Tue, 16 Jun 2020 09:12:35: 17000000 INFO @ Tue, 16 Jun 2020 09:12:40: 22000000 INFO @ Tue, 16 Jun 2020 09:12:43: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:47: 23000000 INFO @ Tue, 16 Jun 2020 09:12:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:50: 19000000 INFO @ Tue, 16 Jun 2020 09:12:55: 24000000 INFO @ Tue, 16 Jun 2020 09:12:57: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 09:12:57: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 09:12:57: #1 total tags in treatment: 11898501 INFO @ Tue, 16 Jun 2020 09:12:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:57: #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 09:12:57: #1 tags after filtering in treatment: 11061583 INFO @ Tue, 16 Jun 2020 09:12:57: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 09:12:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:58: #2 number of paired peaks: 319 WARNING @ Tue, 16 Jun 2020 09:12:58: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:58: #2 predicted fragment length is 214 bps INFO @ Tue, 16 Jun 2020 09:12:58: #2 alternative fragment length(s) may be 214 bps INFO @ Tue, 16 Jun 2020 09:12:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:58: #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 09:12:58: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Tue, 16 Jun 2020 09:12:58: #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 09:12:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:58: 20000000 INFO @ Tue, 16 Jun 2020 09:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.05_summits.bed INFO @ Tue, 16 Jun 2020 09:13:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (413 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:05: 21000000 INFO @ Tue, 16 Jun 2020 09:13:12: 22000000 INFO @ Tue, 16 Jun 2020 09:13:20: 23000000 INFO @ Tue, 16 Jun 2020 09:13:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:27: 24000000 INFO @ Tue, 16 Jun 2020 09:13:28: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 09:13:28: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 09:13:28: #1 total tags in treatment: 11898501 INFO @ Tue, 16 Jun 2020 09:13:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:28: #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 09:13:29: #1 tags after filtering in treatment: 11061583 INFO @ Tue, 16 Jun 2020 09:13:29: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 09:13:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:29: #2 number of paired peaks: 319 WARNING @ Tue, 16 Jun 2020 09:13:29: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:29: #2 predicted fragment length is 214 bps INFO @ Tue, 16 Jun 2020 09:13:29: #2 alternative fragment length(s) may be 214 bps INFO @ Tue, 16 Jun 2020 09:13:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.20_model.r WARNING @ Tue, 16 Jun 2020 09:13:29: #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 09:13:29: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Tue, 16 Jun 2020 09:13:29: #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 09:13:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:32: Done! BigWig に変換しました。 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (325 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3058060/SRX3058060.20_summits.bed INFO @ Tue, 16 Jun 2020 09:14:03: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (237 records, 4 fields): 2 millis CompletedMACS2peakCalling