Job ID = 7097040 SRX = SRX6922977 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27379069 spots for SRR10202923/SRR10202923.sra Written 27379069 spots for SRR10202923/SRR10202923.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:34:32 27379069 reads; of these: 27379069 (100.00%) were unpaired; of these: 949789 (3.47%) aligned 0 times 23324436 (85.19%) aligned exactly 1 time 3104844 (11.34%) aligned >1 times 96.53% overall alignment rate Time searching: 00:34:34 Overall time: 00:34:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3089775 / 26429280 = 0.1169 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 @ Wed, 22 Jul 2020 11:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Jul 2020 11:59:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:59:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:59:19: 1000000 INFO @ Wed, 22 Jul 2020 11:59:24: 2000000 INFO @ Wed, 22 Jul 2020 11:59:30: 3000000 INFO @ Wed, 22 Jul 2020 11:59:36: 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 @ Wed, 22 Jul 2020 11:59:42: 5000000 INFO @ Wed, 22 Jul 2020 11:59:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Jul 2020 11:59:43: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:59:43: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:59:48: 6000000 INFO @ Wed, 22 Jul 2020 11:59:49: 1000000 INFO @ Wed, 22 Jul 2020 11:59:54: 7000000 INFO @ Wed, 22 Jul 2020 11:59:55: 2000000 INFO @ Wed, 22 Jul 2020 12:00:00: 8000000 INFO @ Wed, 22 Jul 2020 12:00:02: 3000000 INFO @ Wed, 22 Jul 2020 12:00:06: 9000000 INFO @ Wed, 22 Jul 2020 12:00:08: 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 @ Wed, 22 Jul 2020 12:00:12: 10000000 INFO @ Wed, 22 Jul 2020 12:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Jul 2020 12:00:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:00:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:00:14: 5000000 INFO @ Wed, 22 Jul 2020 12:00:19: 11000000 INFO @ Wed, 22 Jul 2020 12:00:20: 1000000 INFO @ Wed, 22 Jul 2020 12:00:20: 6000000 INFO @ Wed, 22 Jul 2020 12:00:25: 12000000 INFO @ Wed, 22 Jul 2020 12:00:26: 2000000 INFO @ Wed, 22 Jul 2020 12:00:27: 7000000 INFO @ Wed, 22 Jul 2020 12:00:31: 13000000 INFO @ Wed, 22 Jul 2020 12:00:32: 3000000 INFO @ Wed, 22 Jul 2020 12:00:33: 8000000 INFO @ Wed, 22 Jul 2020 12:00:38: 14000000 INFO @ Wed, 22 Jul 2020 12:00:39: 4000000 INFO @ Wed, 22 Jul 2020 12:00:40: 9000000 INFO @ Wed, 22 Jul 2020 12:00:44: 15000000 INFO @ Wed, 22 Jul 2020 12:00:45: 5000000 INFO @ Wed, 22 Jul 2020 12:00:46: 10000000 INFO @ Wed, 22 Jul 2020 12:00:50: 16000000 INFO @ Wed, 22 Jul 2020 12:00:51: 6000000 INFO @ Wed, 22 Jul 2020 12:00:52: 11000000 INFO @ Wed, 22 Jul 2020 12:00:57: 17000000 INFO @ Wed, 22 Jul 2020 12:00:58: 7000000 INFO @ Wed, 22 Jul 2020 12:00:59: 12000000 INFO @ Wed, 22 Jul 2020 12:01:03: 18000000 INFO @ Wed, 22 Jul 2020 12:01:04: 8000000 INFO @ Wed, 22 Jul 2020 12:01:05: 13000000 INFO @ Wed, 22 Jul 2020 12:01:09: 19000000 INFO @ Wed, 22 Jul 2020 12:01:10: 9000000 INFO @ Wed, 22 Jul 2020 12:01:12: 14000000 INFO @ Wed, 22 Jul 2020 12:01:16: 20000000 INFO @ Wed, 22 Jul 2020 12:01:17: 10000000 INFO @ Wed, 22 Jul 2020 12:01:18: 15000000 INFO @ Wed, 22 Jul 2020 12:01:22: 21000000 INFO @ Wed, 22 Jul 2020 12:01:23: 11000000 INFO @ Wed, 22 Jul 2020 12:01:25: 16000000 INFO @ Wed, 22 Jul 2020 12:01:28: 22000000 INFO @ Wed, 22 Jul 2020 12:01:29: 12000000 INFO @ Wed, 22 Jul 2020 12:01:31: 17000000 INFO @ Wed, 22 Jul 2020 12:01:34: 23000000 INFO @ Wed, 22 Jul 2020 12:01:36: 13000000 INFO @ Wed, 22 Jul 2020 12:01:37: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 12:01:37: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 12:01:37: #1 total tags in treatment: 23339505 INFO @ Wed, 22 Jul 2020 12:01:37: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:01:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:01:37: #1 tags after filtering in treatment: 23339302 INFO @ Wed, 22 Jul 2020 12:01:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:01:37: #1 finished! INFO @ Wed, 22 Jul 2020 12:01:37: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:01:38: 18000000 INFO @ Wed, 22 Jul 2020 12:01:42: #2 number of paired peaks: 86840 INFO @ Wed, 22 Jul 2020 12:01:42: start model_add_line... INFO @ Wed, 22 Jul 2020 12:01:42: start X-correlation... INFO @ Wed, 22 Jul 2020 12:01:42: end of X-cor INFO @ Wed, 22 Jul 2020 12:01:42: #2 finished! INFO @ Wed, 22 Jul 2020 12:01:42: #2 predicted fragment length is 150 bps INFO @ Wed, 22 Jul 2020 12:01:42: #2 alternative fragment length(s) may be 150 bps INFO @ Wed, 22 Jul 2020 12:01:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.05_model.r WARNING @ Wed, 22 Jul 2020 12:01:42: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:01:42: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Wed, 22 Jul 2020 12:01:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:01:42: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:01:43: 14000000 INFO @ Wed, 22 Jul 2020 12:01:44: 19000000 INFO @ Wed, 22 Jul 2020 12:01:49: 15000000 INFO @ Wed, 22 Jul 2020 12:01:51: 20000000 INFO @ Wed, 22 Jul 2020 12:01:56: 16000000 INFO @ Wed, 22 Jul 2020 12:01:57: 21000000 INFO @ Wed, 22 Jul 2020 12:02:02: 17000000 INFO @ Wed, 22 Jul 2020 12:02:03: 22000000 INFO @ Wed, 22 Jul 2020 12:02:09: 18000000 INFO @ Wed, 22 Jul 2020 12:02:09: 23000000 INFO @ Wed, 22 Jul 2020 12:02:12: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 12:02:12: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 12:02:12: #1 total tags in treatment: 23339505 INFO @ Wed, 22 Jul 2020 12:02:12: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:02:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:02:12: #1 tags after filtering in treatment: 23339302 INFO @ Wed, 22 Jul 2020 12:02:12: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:02:12: #1 finished! INFO @ Wed, 22 Jul 2020 12:02:12: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:02:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:02:15: 19000000 INFO @ Wed, 22 Jul 2020 12:02:17: #2 number of paired peaks: 86840 INFO @ Wed, 22 Jul 2020 12:02:17: start model_add_line... INFO @ Wed, 22 Jul 2020 12:02:17: start X-correlation... INFO @ Wed, 22 Jul 2020 12:02:17: end of X-cor INFO @ Wed, 22 Jul 2020 12:02:17: #2 finished! INFO @ Wed, 22 Jul 2020 12:02:17: #2 predicted fragment length is 150 bps INFO @ Wed, 22 Jul 2020 12:02:17: #2 alternative fragment length(s) may be 150 bps INFO @ Wed, 22 Jul 2020 12:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.10_model.r WARNING @ Wed, 22 Jul 2020 12:02:17: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:02:17: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Wed, 22 Jul 2020 12:02:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:02:17: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:02:21: 20000000 INFO @ Wed, 22 Jul 2020 12:02:27: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:02:33: 22000000 INFO @ Wed, 22 Jul 2020 12:02:39: 23000000 INFO @ Wed, 22 Jul 2020 12:02:41: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 12:02:41: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 12:02:41: #1 total tags in treatment: 23339505 INFO @ Wed, 22 Jul 2020 12:02:41: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:02:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:02:41: #1 tags after filtering in treatment: 23339302 INFO @ Wed, 22 Jul 2020 12:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:02:41: #1 finished! INFO @ Wed, 22 Jul 2020 12:02:41: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:02:42: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:02:46: #2 number of paired peaks: 86840 INFO @ Wed, 22 Jul 2020 12:02:46: start model_add_line... INFO @ Wed, 22 Jul 2020 12:02:46: start X-correlation... INFO @ Wed, 22 Jul 2020 12:02:46: end of X-cor INFO @ Wed, 22 Jul 2020 12:02:46: #2 finished! INFO @ Wed, 22 Jul 2020 12:02:46: #2 predicted fragment length is 150 bps INFO @ Wed, 22 Jul 2020 12:02:46: #2 alternative fragment length(s) may be 150 bps INFO @ Wed, 22 Jul 2020 12:02:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.20_model.r WARNING @ Wed, 22 Jul 2020 12:02:46: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:02:46: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Wed, 22 Jul 2020 12:02:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:02:46: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:02:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:03:15: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:03:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:03:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.05_summits.bed INFO @ Wed, 22 Jul 2020 12:03:16: Done! pass1 - making usageList (108 chroms): 6 millis pass2 - checking and writing primary data (45231 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:03:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.10_summits.bed INFO @ Wed, 22 Jul 2020 12:03:49: Done! pass1 - making usageList (86 chroms): 5 millis pass2 - checking and writing primary data (31123 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922977/SRX6922977.20_summits.bed INFO @ Wed, 22 Jul 2020 12:04:18: Done! pass1 - making usageList (65 chroms): 3 millis pass2 - checking and writing primary data (18543 records, 4 fields): 21 millis CompletedMACS2peakCalling