Job ID = 12531443 SRX = SRX3087668 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 118351535 spots for SRR5927304/SRR5927304.sra Written 118351535 spots for SRR5927304/SRR5927304.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:51:47 118351535 reads; of these: 118351535 (100.00%) were unpaired; of these: 18921252 (15.99%) aligned 0 times 70443956 (59.52%) aligned exactly 1 time 28986327 (24.49%) aligned >1 times 84.01% overall alignment rate Time searching: 01:51:52 Overall time: 01:51:52 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 44 files... [bam_rmdupse_core] 72199184 / 99430283 = 0.7261 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.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 @ Sat, 17 Apr 2021 09:54:18: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:54:18: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:54:32: 1000000 INFO @ Sat, 17 Apr 2021 09:54:43: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.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 @ Sat, 17 Apr 2021 09:54:48: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:54:48: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:54:56: 3000000 INFO @ Sat, 17 Apr 2021 09:55:04: 1000000 INFO @ Sat, 17 Apr 2021 09:55:05: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:55:15: 5000000 INFO @ Sat, 17 Apr 2021 09:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.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 @ Sat, 17 Apr 2021 09:55:18: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:55:18: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:55:19: 2000000 INFO @ Sat, 17 Apr 2021 09:55:30: 6000000 INFO @ Sat, 17 Apr 2021 09:55:33: 3000000 INFO @ Sat, 17 Apr 2021 09:55:34: 1000000 INFO @ Sat, 17 Apr 2021 09:55:44: 4000000 INFO @ Sat, 17 Apr 2021 09:55:46: 2000000 INFO @ Sat, 17 Apr 2021 09:55:50: 7000000 INFO @ Sat, 17 Apr 2021 09:55:58: 5000000 INFO @ Sat, 17 Apr 2021 09:55:59: 3000000 INFO @ Sat, 17 Apr 2021 09:56:08: 8000000 INFO @ Sat, 17 Apr 2021 09:56:12: 6000000 INFO @ Sat, 17 Apr 2021 09:56:12: 4000000 INFO @ Sat, 17 Apr 2021 09:56:23: 7000000 INFO @ Sat, 17 Apr 2021 09:56:24: 5000000 INFO @ Sat, 17 Apr 2021 09:56:28: 9000000 INFO @ Sat, 17 Apr 2021 09:56:37: 8000000 INFO @ Sat, 17 Apr 2021 09:56:37: 6000000 INFO @ Sat, 17 Apr 2021 09:56:45: 10000000 INFO @ Sat, 17 Apr 2021 09:56:49: 7000000 INFO @ Sat, 17 Apr 2021 09:56:52: 9000000 INFO @ Sat, 17 Apr 2021 09:57:01: 11000000 INFO @ Sat, 17 Apr 2021 09:57:03: 8000000 INFO @ Sat, 17 Apr 2021 09:57:06: 10000000 INFO @ Sat, 17 Apr 2021 09:57:13: 12000000 INFO @ Sat, 17 Apr 2021 09:57:16: 9000000 INFO @ Sat, 17 Apr 2021 09:57:20: 11000000 INFO @ Sat, 17 Apr 2021 09:57:29: 10000000 INFO @ Sat, 17 Apr 2021 09:57:29: 13000000 INFO @ Sat, 17 Apr 2021 09:57:35: 12000000 INFO @ Sat, 17 Apr 2021 09:57:41: 11000000 INFO @ Sat, 17 Apr 2021 09:57:44: 14000000 INFO @ Sat, 17 Apr 2021 09:57:48: 13000000 INFO @ Sat, 17 Apr 2021 09:57:54: 12000000 INFO @ Sat, 17 Apr 2021 09:57:59: 15000000 INFO @ Sat, 17 Apr 2021 09:58:02: 14000000 INFO @ Sat, 17 Apr 2021 09:58:07: 13000000 INFO @ Sat, 17 Apr 2021 09:58:12: 16000000 INFO @ Sat, 17 Apr 2021 09:58:17: 15000000 INFO @ Sat, 17 Apr 2021 09:58:21: 14000000 INFO @ Sat, 17 Apr 2021 09:58:26: 17000000 INFO @ Sat, 17 Apr 2021 09:58:34: 15000000 INFO @ Sat, 17 Apr 2021 09:58:41: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:58:43: 18000000 INFO @ Sat, 17 Apr 2021 09:58:56: 16000000 INFO @ Sat, 17 Apr 2021 09:58:56: 19000000 INFO @ Sat, 17 Apr 2021 09:59:05: 17000000 INFO @ Sat, 17 Apr 2021 09:59:12: 20000000 INFO @ Sat, 17 Apr 2021 09:59:19: 18000000 INFO @ Sat, 17 Apr 2021 09:59:19: 17000000 INFO @ Sat, 17 Apr 2021 09:59:27: 21000000 INFO @ Sat, 17 Apr 2021 09:59:32: 19000000 INFO @ Sat, 17 Apr 2021 09:59:36: 18000000 INFO @ Sat, 17 Apr 2021 09:59:41: 22000000 INFO @ Sat, 17 Apr 2021 09:59:43: 20000000 INFO @ Sat, 17 Apr 2021 09:59:52: 19000000 INFO @ Sat, 17 Apr 2021 09:59:55: 23000000 INFO @ Sat, 17 Apr 2021 09:59:56: 21000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 10:00:08: 24000000 INFO @ Sat, 17 Apr 2021 10:00:09: 20000000 INFO @ Sat, 17 Apr 2021 10:00:09: 22000000 INFO @ Sat, 17 Apr 2021 10:00:24: 23000000 INFO @ Sat, 17 Apr 2021 10:00:24: 25000000 INFO @ Sat, 17 Apr 2021 10:00:29: 21000000 INFO @ Sat, 17 Apr 2021 10:00:38: 24000000 INFO @ Sat, 17 Apr 2021 10:00:42: 26000000 INFO @ Sat, 17 Apr 2021 10:00:46: 22000000 INFO @ Sat, 17 Apr 2021 10:00:52: 25000000 INFO @ Sat, 17 Apr 2021 10:00:59: 27000000 INFO @ Sat, 17 Apr 2021 10:01:05: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 10:01:05: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 10:01:05: #1 total tags in treatment: 27231099 INFO @ Sat, 17 Apr 2021 10:01:05: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 10:01:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 10:01:05: 26000000 INFO @ Sat, 17 Apr 2021 10:01:05: #1 tags after filtering in treatment: 27231000 INFO @ Sat, 17 Apr 2021 10:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 10:01:05: #1 finished! INFO @ Sat, 17 Apr 2021 10:01:05: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 10:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 10:01:09: 23000000 INFO @ Sat, 17 Apr 2021 10:01:10: #2 number of paired peaks: 60954 INFO @ Sat, 17 Apr 2021 10:01:10: start model_add_line... INFO @ Sat, 17 Apr 2021 10:01:11: start X-correlation... INFO @ Sat, 17 Apr 2021 10:01:11: end of X-cor INFO @ Sat, 17 Apr 2021 10:01:11: #2 finished! INFO @ Sat, 17 Apr 2021 10:01:11: #2 predicted fragment length is 112 bps INFO @ Sat, 17 Apr 2021 10:01:11: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 17 Apr 2021 10:01:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.05_model.r WARNING @ Sat, 17 Apr 2021 10:01:11: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 10:01:11: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 17 Apr 2021 10:01:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 10:01:11: #3 Call peaks... INFO @ Sat, 17 Apr 2021 10:01:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 10:01:19: 27000000 INFO @ Sat, 17 Apr 2021 10:01:23: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 10:01:23: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 10:01:23: #1 total tags in treatment: 27231099 INFO @ Sat, 17 Apr 2021 10:01:23: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 10:01:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 10:01:24: #1 tags after filtering in treatment: 27231000 INFO @ Sat, 17 Apr 2021 10:01:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 10:01:24: #1 finished! INFO @ Sat, 17 Apr 2021 10:01:24: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 10:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 10:01:29: #2 number of paired peaks: 60954 INFO @ Sat, 17 Apr 2021 10:01:29: start model_add_line... INFO @ Sat, 17 Apr 2021 10:01:29: start X-correlation... INFO @ Sat, 17 Apr 2021 10:01:29: end of X-cor INFO @ Sat, 17 Apr 2021 10:01:29: #2 finished! INFO @ Sat, 17 Apr 2021 10:01:29: #2 predicted fragment length is 112 bps INFO @ Sat, 17 Apr 2021 10:01:29: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 17 Apr 2021 10:01:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.10_model.r WARNING @ Sat, 17 Apr 2021 10:01:29: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 10:01:29: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 17 Apr 2021 10:01:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 10:01:29: #3 Call peaks... INFO @ Sat, 17 Apr 2021 10:01:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 10:01:35: 24000000 INFO @ Sat, 17 Apr 2021 10:01:51: 25000000 INFO @ Sat, 17 Apr 2021 10:02:08: 26000000 INFO @ Sat, 17 Apr 2021 10:02:21: 27000000 INFO @ Sat, 17 Apr 2021 10:02:25: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 10:02:25: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 10:02:25: #1 total tags in treatment: 27231099 INFO @ Sat, 17 Apr 2021 10:02:25: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 10:02:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 10:02:26: #1 tags after filtering in treatment: 27231000 INFO @ Sat, 17 Apr 2021 10:02:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 10:02:26: #1 finished! INFO @ Sat, 17 Apr 2021 10:02:26: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 10:02:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 10:02:31: #2 number of paired peaks: 60954 INFO @ Sat, 17 Apr 2021 10:02:31: start model_add_line... INFO @ Sat, 17 Apr 2021 10:02:31: start X-correlation... INFO @ Sat, 17 Apr 2021 10:02:31: end of X-cor INFO @ Sat, 17 Apr 2021 10:02:31: #2 finished! INFO @ Sat, 17 Apr 2021 10:02:31: #2 predicted fragment length is 112 bps INFO @ Sat, 17 Apr 2021 10:02:31: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 17 Apr 2021 10:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.20_model.r WARNING @ Sat, 17 Apr 2021 10:02:31: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 10:02:31: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 17 Apr 2021 10:02:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 10:02:31: #3 Call peaks... INFO @ Sat, 17 Apr 2021 10:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 10:02:37: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 10:02:52: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 10:03:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.10_peaks.xls INFO @ Sat, 17 Apr 2021 10:03:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 10:03:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.10_summits.bed INFO @ Sat, 17 Apr 2021 10:03:41: Done! pass1 - making usageList (132 chroms): 10 millis pass2 - checking and writing primary data (33965 records, 4 fields): 75 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 10:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.05_peaks.xls INFO @ Sat, 17 Apr 2021 10:03:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 10:03:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.05_summits.bed INFO @ Sat, 17 Apr 2021 10:03:51: Done! pass1 - making usageList (173 chroms): 23 millis pass2 - checking and writing primary data (56585 records, 4 fields): 89 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 10:03:56: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 10:04:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.20_peaks.xls INFO @ Sat, 17 Apr 2021 10:04:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 10:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087668/SRX3087668.20_summits.bed INFO @ Sat, 17 Apr 2021 10:04:45: Done! pass1 - making usageList (89 chroms): 6 millis pass2 - checking and writing primary data (15669 records, 4 fields): 28 millis CompletedMACS2peakCalling