Job ID = 6367844 SRX = SRX4085412 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:47:44 prefetch.2.10.7: 1) Downloading 'SRR7167441'... 2020-06-15T23:47:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:13 prefetch.2.10.7: 1) 'SRR7167441' was downloaded successfully Read 21947298 spots for SRR7167441/SRR7167441.sra Written 21947298 spots for SRR7167441/SRR7167441.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: 00:13:25 21947298 reads; of these: 21947298 (100.00%) were paired; of these: 11556844 (52.66%) aligned concordantly 0 times 8526932 (38.85%) aligned concordantly exactly 1 time 1863522 (8.49%) aligned concordantly >1 times ---- 11556844 pairs aligned concordantly 0 times; of these: 430263 (3.72%) aligned discordantly 1 time ---- 11126581 pairs aligned 0 times concordantly or discordantly; of these: 22253162 mates make up the pairs; of these: 17030235 (76.53%) aligned 0 times 4623521 (20.78%) aligned exactly 1 time 599406 (2.69%) aligned >1 times 61.20% overall alignment rate Time searching: 00:13:25 Overall time: 00:13:25 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] 1435276 / 10662719 = 0.1346 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 09:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.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 09:17:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:44: 1000000 INFO @ Tue, 16 Jun 2020 09:17:50: 2000000 INFO @ Tue, 16 Jun 2020 09:17:56: 3000000 INFO @ Tue, 16 Jun 2020 09:18:02: 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 09:18:07: 5000000 INFO @ Tue, 16 Jun 2020 09:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.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 09:18:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:14: 6000000 INFO @ Tue, 16 Jun 2020 09:18:14: 1000000 INFO @ Tue, 16 Jun 2020 09:18:20: 7000000 INFO @ Tue, 16 Jun 2020 09:18:20: 2000000 INFO @ Tue, 16 Jun 2020 09:18:26: 8000000 INFO @ Tue, 16 Jun 2020 09:18:26: 3000000 INFO @ Tue, 16 Jun 2020 09:18:32: 9000000 INFO @ Tue, 16 Jun 2020 09:18:33: 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 09:18:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.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 09:18:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:38: 10000000 INFO @ Tue, 16 Jun 2020 09:18:39: 5000000 INFO @ Tue, 16 Jun 2020 09:18:44: 1000000 INFO @ Tue, 16 Jun 2020 09:18:45: 11000000 INFO @ Tue, 16 Jun 2020 09:18:45: 6000000 INFO @ Tue, 16 Jun 2020 09:18:51: 2000000 INFO @ Tue, 16 Jun 2020 09:18:52: 12000000 INFO @ Tue, 16 Jun 2020 09:18:52: 7000000 INFO @ Tue, 16 Jun 2020 09:18:57: 3000000 INFO @ Tue, 16 Jun 2020 09:18:58: 13000000 INFO @ Tue, 16 Jun 2020 09:18:58: 8000000 INFO @ Tue, 16 Jun 2020 09:19:04: 4000000 INFO @ Tue, 16 Jun 2020 09:19:05: 14000000 INFO @ Tue, 16 Jun 2020 09:19:05: 9000000 INFO @ Tue, 16 Jun 2020 09:19:10: 5000000 INFO @ Tue, 16 Jun 2020 09:19:11: 15000000 INFO @ Tue, 16 Jun 2020 09:19:12: 10000000 INFO @ Tue, 16 Jun 2020 09:19:17: 6000000 INFO @ Tue, 16 Jun 2020 09:19:18: 16000000 INFO @ Tue, 16 Jun 2020 09:19:18: 11000000 INFO @ Tue, 16 Jun 2020 09:19:23: 7000000 INFO @ Tue, 16 Jun 2020 09:19:24: 17000000 INFO @ Tue, 16 Jun 2020 09:19:25: 12000000 INFO @ Tue, 16 Jun 2020 09:19:30: 8000000 INFO @ Tue, 16 Jun 2020 09:19:30: 18000000 INFO @ Tue, 16 Jun 2020 09:19:32: 13000000 INFO @ Tue, 16 Jun 2020 09:19:37: 9000000 INFO @ Tue, 16 Jun 2020 09:19:37: 19000000 INFO @ Tue, 16 Jun 2020 09:19:38: 14000000 INFO @ Tue, 16 Jun 2020 09:19:43: 20000000 INFO @ Tue, 16 Jun 2020 09:19:43: 10000000 INFO @ Tue, 16 Jun 2020 09:19:45: 15000000 INFO @ Tue, 16 Jun 2020 09:19:50: 21000000 INFO @ Tue, 16 Jun 2020 09:19:50: 11000000 INFO @ Tue, 16 Jun 2020 09:19:51: 16000000 INFO @ Tue, 16 Jun 2020 09:19:56: 22000000 INFO @ Tue, 16 Jun 2020 09:19:56: 12000000 INFO @ Tue, 16 Jun 2020 09:19:57: 17000000 INFO @ Tue, 16 Jun 2020 09:20:02: 23000000 INFO @ Tue, 16 Jun 2020 09:20:03: 13000000 INFO @ Tue, 16 Jun 2020 09:20:04: 18000000 INFO @ Tue, 16 Jun 2020 09:20:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:08: #1 total tags in treatment: 8992812 INFO @ Tue, 16 Jun 2020 09:20:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:08: #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 09:20:08: #1 tags after filtering in treatment: 7238212 INFO @ Tue, 16 Jun 2020 09:20:08: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 09:20:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:09: #2 number of paired peaks: 942 WARNING @ Tue, 16 Jun 2020 09:20:09: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:09: #2 predicted fragment length is 86 bps INFO @ Tue, 16 Jun 2020 09:20:09: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 16 Jun 2020 09:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:09: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:09: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 16 Jun 2020 09:20:09: #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 09:20:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:09: 14000000 INFO @ Tue, 16 Jun 2020 09:20:11: 19000000 INFO @ Tue, 16 Jun 2020 09:20:15: 15000000 INFO @ Tue, 16 Jun 2020 09:20:17: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:22: 16000000 INFO @ Tue, 16 Jun 2020 09:20:23: 21000000 INFO @ Tue, 16 Jun 2020 09:20:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:28: 17000000 INFO @ Tue, 16 Jun 2020 09:20:30: 22000000 INFO @ Tue, 16 Jun 2020 09:20:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:34: Done! INFO @ Tue, 16 Jun 2020 09:20:34: 18000000 pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7653 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:35: 23000000 INFO @ Tue, 16 Jun 2020 09:20:41: 19000000 INFO @ Tue, 16 Jun 2020 09:20:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:41: #1 total tags in treatment: 8992812 INFO @ Tue, 16 Jun 2020 09:20:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:41: #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 09:20:41: #1 tags after filtering in treatment: 7238212 INFO @ Tue, 16 Jun 2020 09:20:41: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 09:20:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:42: #2 number of paired peaks: 942 WARNING @ Tue, 16 Jun 2020 09:20:42: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:42: #2 predicted fragment length is 86 bps INFO @ Tue, 16 Jun 2020 09:20:42: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 16 Jun 2020 09:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:42: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:42: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 16 Jun 2020 09:20:42: #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 09:20:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:47: 20000000 INFO @ Tue, 16 Jun 2020 09:20:53: 21000000 INFO @ Tue, 16 Jun 2020 09:20:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:59: 22000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:04: 23000000 INFO @ Tue, 16 Jun 2020 09:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4812 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:10: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:10: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:10: #1 total tags in treatment: 8992812 INFO @ Tue, 16 Jun 2020 09:21:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:10: #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 09:21:10: #1 tags after filtering in treatment: 7238212 INFO @ Tue, 16 Jun 2020 09:21:10: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 09:21:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:10: #2 number of paired peaks: 942 WARNING @ Tue, 16 Jun 2020 09:21:10: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:11: #2 predicted fragment length is 86 bps INFO @ Tue, 16 Jun 2020 09:21:11: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 16 Jun 2020 09:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:11: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:11: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 16 Jun 2020 09:21:11: #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 09:21:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085412/SRX4085412.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2514 records, 4 fields): 8 millis CompletedMACS2peakCalling