Job ID = 6497389 SRX = SRX4085369 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:13:40 prefetch.2.10.7: 1) Downloading 'SRR7167398'... 2020-06-25T22:13:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:18:51 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:18:51 prefetch.2.10.7: 1) 'SRR7167398' was downloaded successfully Read 20071556 spots for SRR7167398/SRR7167398.sra Written 20071556 spots for SRR7167398/SRR7167398.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: 00:13:43 20071556 reads; of these: 20071556 (100.00%) were paired; of these: 6782410 (33.79%) aligned concordantly 0 times 11622833 (57.91%) aligned concordantly exactly 1 time 1666313 (8.30%) aligned concordantly >1 times ---- 6782410 pairs aligned concordantly 0 times; of these: 346860 (5.11%) aligned discordantly 1 time ---- 6435550 pairs aligned 0 times concordantly or discordantly; of these: 12871100 mates make up the pairs; of these: 9942528 (77.25%) aligned 0 times 2580543 (20.05%) aligned exactly 1 time 348029 (2.70%) aligned >1 times 75.23% overall alignment rate Time searching: 00:13:43 Overall time: 00:13:43 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 16 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] 1149757 / 13515966 = 0.0851 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 @ Fri, 26 Jun 2020 07:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.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 @ Fri, 26 Jun 2020 07:43:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:43:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:43:31: 1000000 INFO @ Fri, 26 Jun 2020 07:43:37: 2000000 INFO @ Fri, 26 Jun 2020 07:43:43: 3000000 INFO @ Fri, 26 Jun 2020 07:43:49: 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 @ Fri, 26 Jun 2020 07:43:54: 5000000 INFO @ Fri, 26 Jun 2020 07:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.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 @ Fri, 26 Jun 2020 07:43:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:43:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:44:01: 6000000 INFO @ Fri, 26 Jun 2020 07:44:03: 1000000 INFO @ Fri, 26 Jun 2020 07:44:08: 7000000 INFO @ Fri, 26 Jun 2020 07:44:11: 2000000 INFO @ Fri, 26 Jun 2020 07:44:14: 8000000 INFO @ Fri, 26 Jun 2020 07:44:19: 3000000 INFO @ Fri, 26 Jun 2020 07:44:21: 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 @ Fri, 26 Jun 2020 07:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.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 @ Fri, 26 Jun 2020 07:44:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:44:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:44:27: 4000000 INFO @ Fri, 26 Jun 2020 07:44:28: 10000000 INFO @ Fri, 26 Jun 2020 07:44:33: 1000000 INFO @ Fri, 26 Jun 2020 07:44:34: 11000000 INFO @ Fri, 26 Jun 2020 07:44:35: 5000000 INFO @ Fri, 26 Jun 2020 07:44:41: 12000000 INFO @ Fri, 26 Jun 2020 07:44:41: 2000000 INFO @ Fri, 26 Jun 2020 07:44:43: 6000000 INFO @ Fri, 26 Jun 2020 07:44:48: 13000000 INFO @ Fri, 26 Jun 2020 07:44:49: 3000000 INFO @ Fri, 26 Jun 2020 07:44:51: 7000000 INFO @ Fri, 26 Jun 2020 07:44:54: 14000000 INFO @ Fri, 26 Jun 2020 07:44:57: 4000000 INFO @ Fri, 26 Jun 2020 07:44:59: 8000000 INFO @ Fri, 26 Jun 2020 07:45:01: 15000000 INFO @ Fri, 26 Jun 2020 07:45:05: 5000000 INFO @ Fri, 26 Jun 2020 07:45:07: 9000000 INFO @ Fri, 26 Jun 2020 07:45:08: 16000000 INFO @ Fri, 26 Jun 2020 07:45:13: 6000000 INFO @ Fri, 26 Jun 2020 07:45:14: 17000000 INFO @ Fri, 26 Jun 2020 07:45:14: 10000000 INFO @ Fri, 26 Jun 2020 07:45:21: 18000000 INFO @ Fri, 26 Jun 2020 07:45:21: 7000000 INFO @ Fri, 26 Jun 2020 07:45:22: 11000000 INFO @ Fri, 26 Jun 2020 07:45:27: 19000000 INFO @ Fri, 26 Jun 2020 07:45:29: 8000000 INFO @ Fri, 26 Jun 2020 07:45:30: 12000000 INFO @ Fri, 26 Jun 2020 07:45:34: 20000000 INFO @ Fri, 26 Jun 2020 07:45:37: 9000000 INFO @ Fri, 26 Jun 2020 07:45:38: 13000000 INFO @ Fri, 26 Jun 2020 07:45:41: 21000000 INFO @ Fri, 26 Jun 2020 07:45:44: 10000000 INFO @ Fri, 26 Jun 2020 07:45:45: 14000000 INFO @ Fri, 26 Jun 2020 07:45:47: 22000000 INFO @ Fri, 26 Jun 2020 07:45:52: 11000000 INFO @ Fri, 26 Jun 2020 07:45:53: 15000000 INFO @ Fri, 26 Jun 2020 07:45:54: 23000000 INFO @ Fri, 26 Jun 2020 07:46:00: 12000000 INFO @ Fri, 26 Jun 2020 07:46:01: 24000000 INFO @ Fri, 26 Jun 2020 07:46:01: 16000000 INFO @ Fri, 26 Jun 2020 07:46:07: 25000000 INFO @ Fri, 26 Jun 2020 07:46:08: 13000000 INFO @ Fri, 26 Jun 2020 07:46:09: 17000000 INFO @ Fri, 26 Jun 2020 07:46:14: 26000000 INFO @ Fri, 26 Jun 2020 07:46:15: 14000000 INFO @ Fri, 26 Jun 2020 07:46:16: 18000000 INFO @ Fri, 26 Jun 2020 07:46:20: 27000000 INFO @ Fri, 26 Jun 2020 07:46:23: 15000000 INFO @ Fri, 26 Jun 2020 07:46:24: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:46:26: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:46:26: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:46:26: #1 total tags in treatment: 12158559 INFO @ Fri, 26 Jun 2020 07:46:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:46:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:46:26: #1 tags after filtering in treatment: 10404588 INFO @ Fri, 26 Jun 2020 07:46:26: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 07:46:26: #1 finished! INFO @ Fri, 26 Jun 2020 07:46:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:46:27: #2 number of paired peaks: 352 WARNING @ Fri, 26 Jun 2020 07:46:27: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Fri, 26 Jun 2020 07:46:27: start model_add_line... INFO @ Fri, 26 Jun 2020 07:46:27: start X-correlation... INFO @ Fri, 26 Jun 2020 07:46:27: end of X-cor INFO @ Fri, 26 Jun 2020 07:46:27: #2 finished! INFO @ Fri, 26 Jun 2020 07:46:27: #2 predicted fragment length is 82 bps INFO @ Fri, 26 Jun 2020 07:46:27: #2 alternative fragment length(s) may be 82 bps INFO @ Fri, 26 Jun 2020 07:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.05_model.r WARNING @ Fri, 26 Jun 2020 07:46:27: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:46:27: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Fri, 26 Jun 2020 07:46:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:46:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:46:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:46:30: 16000000 INFO @ Fri, 26 Jun 2020 07:46:31: 20000000 INFO @ Fri, 26 Jun 2020 07:46:37: 17000000 INFO @ Fri, 26 Jun 2020 07:46:38: 21000000 INFO @ Fri, 26 Jun 2020 07:46:44: 18000000 INFO @ Fri, 26 Jun 2020 07:46:45: 22000000 INFO @ Fri, 26 Jun 2020 07:46:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:46:51: 19000000 INFO @ Fri, 26 Jun 2020 07:46:52: 23000000 INFO @ Fri, 26 Jun 2020 07:46:58: 20000000 INFO @ Fri, 26 Jun 2020 07:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:46:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:46:59: 24000000 INFO @ Fri, 26 Jun 2020 07:46:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.05_summits.bed INFO @ Fri, 26 Jun 2020 07:46:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4617 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:47:05: 21000000 INFO @ Fri, 26 Jun 2020 07:47:05: 25000000 INFO @ Fri, 26 Jun 2020 07:47:11: 22000000 INFO @ Fri, 26 Jun 2020 07:47:12: 26000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:47:18: 23000000 INFO @ Fri, 26 Jun 2020 07:47:19: 27000000 INFO @ Fri, 26 Jun 2020 07:47:25: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:47:25: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:47:25: #1 total tags in treatment: 12158559 INFO @ Fri, 26 Jun 2020 07:47:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:47:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:47:25: #1 tags after filtering in treatment: 10404588 INFO @ Fri, 26 Jun 2020 07:47:25: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 07:47:25: #1 finished! INFO @ Fri, 26 Jun 2020 07:47:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:47:25: 24000000 INFO @ Fri, 26 Jun 2020 07:47:26: #2 number of paired peaks: 352 WARNING @ Fri, 26 Jun 2020 07:47:26: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Fri, 26 Jun 2020 07:47:26: start model_add_line... INFO @ Fri, 26 Jun 2020 07:47:26: start X-correlation... INFO @ Fri, 26 Jun 2020 07:47:26: end of X-cor INFO @ Fri, 26 Jun 2020 07:47:26: #2 finished! INFO @ Fri, 26 Jun 2020 07:47:26: #2 predicted fragment length is 82 bps INFO @ Fri, 26 Jun 2020 07:47:26: #2 alternative fragment length(s) may be 82 bps INFO @ Fri, 26 Jun 2020 07:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.10_model.r WARNING @ Fri, 26 Jun 2020 07:47:26: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:47:26: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Fri, 26 Jun 2020 07:47:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:47:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:47:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:47:32: 25000000 INFO @ Fri, 26 Jun 2020 07:47:38: 26000000 INFO @ Fri, 26 Jun 2020 07:47:45: 27000000 INFO @ Fri, 26 Jun 2020 07:47:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:47:50: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:47:50: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:47:50: #1 total tags in treatment: 12158559 INFO @ Fri, 26 Jun 2020 07:47:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:47:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:47:50: #1 tags after filtering in treatment: 10404588 INFO @ Fri, 26 Jun 2020 07:47:50: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 07:47:50: #1 finished! INFO @ Fri, 26 Jun 2020 07:47:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:47:51: #2 number of paired peaks: 352 WARNING @ Fri, 26 Jun 2020 07:47:51: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Fri, 26 Jun 2020 07:47:51: start model_add_line... INFO @ Fri, 26 Jun 2020 07:47:51: start X-correlation... INFO @ Fri, 26 Jun 2020 07:47:51: end of X-cor INFO @ Fri, 26 Jun 2020 07:47:51: #2 finished! INFO @ Fri, 26 Jun 2020 07:47:51: #2 predicted fragment length is 82 bps INFO @ Fri, 26 Jun 2020 07:47:51: #2 alternative fragment length(s) may be 82 bps INFO @ Fri, 26 Jun 2020 07:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.20_model.r WARNING @ Fri, 26 Jun 2020 07:47:51: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:47:51: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Fri, 26 Jun 2020 07:47:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:47:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:47:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.10_summits.bed INFO @ Fri, 26 Jun 2020 07:47:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2608 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:48:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:48:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:48:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:48:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085369/SRX4085369.20_summits.bed INFO @ Fri, 26 Jun 2020 07:48:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1121 records, 4 fields): 3 millis CompletedMACS2peakCalling