Job ID = 12531439 SRX = SRX3087664 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 123350687 spots for SRR6445103/SRR6445103.sra Written 123350687 spots for SRR6445103/SRR6445103.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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:36:19 123350687 reads; of these: 123350687 (100.00%) were unpaired; of these: 34172105 (27.70%) aligned 0 times 62717563 (50.84%) aligned exactly 1 time 26461019 (21.45%) aligned >1 times 72.30% overall alignment rate Time searching: 01:36:24 Overall time: 01:36:24 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 40 files... [bam_rmdupse_core] 69094094 / 89178582 = 0.7748 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 09:31:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.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 09:31:54: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:31:54: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:32:02: 1000000 INFO @ Sat, 17 Apr 2021 09:32:10: 2000000 INFO @ Sat, 17 Apr 2021 09:32:18: 3000000 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 09:32:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.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 09:32:24: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:32:24: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:32:26: 4000000 INFO @ Sat, 17 Apr 2021 09:32:31: 1000000 INFO @ Sat, 17 Apr 2021 09:32:34: 5000000 INFO @ Sat, 17 Apr 2021 09:32:39: 2000000 INFO @ Sat, 17 Apr 2021 09:32:42: 6000000 INFO @ Sat, 17 Apr 2021 09:32:46: 3000000 INFO @ Sat, 17 Apr 2021 09:32:51: 7000000 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 09:32:54: 4000000 INFO @ Sat, 17 Apr 2021 09:32:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.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 09:32:54: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:32:54: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:32:59: 8000000 INFO @ Sat, 17 Apr 2021 09:33:01: 5000000 INFO @ Sat, 17 Apr 2021 09:33:01: 1000000 INFO @ Sat, 17 Apr 2021 09:33:07: 9000000 INFO @ Sat, 17 Apr 2021 09:33:09: 6000000 INFO @ Sat, 17 Apr 2021 09:33:09: 2000000 INFO @ Sat, 17 Apr 2021 09:33:15: 10000000 INFO @ Sat, 17 Apr 2021 09:33:16: 7000000 INFO @ Sat, 17 Apr 2021 09:33:17: 3000000 INFO @ Sat, 17 Apr 2021 09:33:23: 11000000 INFO @ Sat, 17 Apr 2021 09:33:24: 8000000 INFO @ Sat, 17 Apr 2021 09:33:24: 4000000 INFO @ Sat, 17 Apr 2021 09:33:31: 12000000 INFO @ Sat, 17 Apr 2021 09:33:32: 9000000 INFO @ Sat, 17 Apr 2021 09:33:32: 5000000 INFO @ Sat, 17 Apr 2021 09:33:39: 13000000 INFO @ Sat, 17 Apr 2021 09:33:40: 10000000 INFO @ Sat, 17 Apr 2021 09:33:40: 6000000 INFO @ Sat, 17 Apr 2021 09:33:47: 11000000 INFO @ Sat, 17 Apr 2021 09:33:47: 7000000 INFO @ Sat, 17 Apr 2021 09:33:48: 14000000 INFO @ Sat, 17 Apr 2021 09:33:55: 12000000 INFO @ Sat, 17 Apr 2021 09:33:55: 8000000 INFO @ Sat, 17 Apr 2021 09:33:56: 15000000 INFO @ Sat, 17 Apr 2021 09:34:02: 13000000 INFO @ Sat, 17 Apr 2021 09:34:02: 9000000 INFO @ Sat, 17 Apr 2021 09:34:04: 16000000 INFO @ Sat, 17 Apr 2021 09:34:10: 14000000 INFO @ Sat, 17 Apr 2021 09:34:10: 10000000 INFO @ Sat, 17 Apr 2021 09:34:12: 17000000 INFO @ Sat, 17 Apr 2021 09:34:18: 15000000 INFO @ Sat, 17 Apr 2021 09:34:18: 11000000 INFO @ Sat, 17 Apr 2021 09:34:20: 18000000 INFO @ Sat, 17 Apr 2021 09:34:25: 16000000 INFO @ Sat, 17 Apr 2021 09:34:25: 12000000 INFO @ Sat, 17 Apr 2021 09:34:29: 19000000 INFO @ Sat, 17 Apr 2021 09:34:33: 17000000 INFO @ Sat, 17 Apr 2021 09:34:33: 13000000 INFO @ Sat, 17 Apr 2021 09:34:37: 20000000 INFO @ Sat, 17 Apr 2021 09:34:38: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 09:34:38: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 09:34:38: #1 total tags in treatment: 20084488 INFO @ Sat, 17 Apr 2021 09:34:38: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:34:38: #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 09:34:38: #1 tags after filtering in treatment: 20084373 INFO @ Sat, 17 Apr 2021 09:34:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 09:34:38: #1 finished! INFO @ Sat, 17 Apr 2021 09:34:38: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:34:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:34:40: 18000000 INFO @ Sat, 17 Apr 2021 09:34:40: 14000000 INFO @ Sat, 17 Apr 2021 09:34:42: #2 number of paired peaks: 29371 INFO @ Sat, 17 Apr 2021 09:34:42: start model_add_line... INFO @ Sat, 17 Apr 2021 09:34:42: start X-correlation... INFO @ Sat, 17 Apr 2021 09:34:42: end of X-cor INFO @ Sat, 17 Apr 2021 09:34:42: #2 finished! INFO @ Sat, 17 Apr 2021 09:34:42: #2 predicted fragment length is 97 bps INFO @ Sat, 17 Apr 2021 09:34:42: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 17 Apr 2021 09:34:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.05_model.r WARNING @ Sat, 17 Apr 2021 09:34:42: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:34:42: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 17 Apr 2021 09:34:42: #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 09:34:42: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:34:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:34:47: 19000000 INFO @ Sat, 17 Apr 2021 09:34:47: 15000000 INFO @ Sat, 17 Apr 2021 09:34:54: 20000000 INFO @ Sat, 17 Apr 2021 09:34:54: 16000000 INFO @ Sat, 17 Apr 2021 09:34:55: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 09:34:55: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 09:34:55: #1 total tags in treatment: 20084488 INFO @ Sat, 17 Apr 2021 09:34:55: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:34:55: #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 09:34:56: #1 tags after filtering in treatment: 20084373 INFO @ Sat, 17 Apr 2021 09:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 09:34:56: #1 finished! INFO @ Sat, 17 Apr 2021 09:34:56: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:34:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:34:59: #2 number of paired peaks: 29371 INFO @ Sat, 17 Apr 2021 09:34:59: start model_add_line... INFO @ Sat, 17 Apr 2021 09:34:59: start X-correlation... INFO @ Sat, 17 Apr 2021 09:34:59: end of X-cor INFO @ Sat, 17 Apr 2021 09:34:59: #2 finished! INFO @ Sat, 17 Apr 2021 09:34:59: #2 predicted fragment length is 97 bps INFO @ Sat, 17 Apr 2021 09:34:59: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 17 Apr 2021 09:34:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.10_model.r WARNING @ Sat, 17 Apr 2021 09:34:59: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:34:59: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 17 Apr 2021 09:34:59: #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 09:34:59: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:35:01: 17000000 INFO @ Sat, 17 Apr 2021 09:35:08: 18000000 INFO @ Sat, 17 Apr 2021 09:35:15: 19000000 INFO @ Sat, 17 Apr 2021 09:35:22: 20000000 INFO @ Sat, 17 Apr 2021 09:35:22: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 09:35:22: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 09:35:22: #1 total tags in treatment: 20084488 INFO @ Sat, 17 Apr 2021 09:35:22: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:35:22: #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 09:35:23: #1 tags after filtering in treatment: 20084373 INFO @ Sat, 17 Apr 2021 09:35:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 09:35:23: #1 finished! INFO @ Sat, 17 Apr 2021 09:35:23: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:35:27: #2 number of paired peaks: 29371 INFO @ Sat, 17 Apr 2021 09:35:27: start model_add_line... INFO @ Sat, 17 Apr 2021 09:35:27: start X-correlation... INFO @ Sat, 17 Apr 2021 09:35:27: end of X-cor INFO @ Sat, 17 Apr 2021 09:35:27: #2 finished! INFO @ Sat, 17 Apr 2021 09:35:27: #2 predicted fragment length is 97 bps INFO @ Sat, 17 Apr 2021 09:35:27: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 17 Apr 2021 09:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.20_model.r WARNING @ Sat, 17 Apr 2021 09:35:27: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:35:27: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 17 Apr 2021 09:35:27: #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 09:35:27: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:35:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:35:53: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:36:07: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.05_summits.bed INFO @ Sat, 17 Apr 2021 09:36:30: Done! pass1 - making usageList (97 chroms): 4 millis pass2 - checking and writing primary data (18578 records, 4 fields): 27 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:36:33: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:36:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.10_summits.bed INFO @ Sat, 17 Apr 2021 09:36:42: Done! pass1 - making usageList (68 chroms): 3 millis pass2 - checking and writing primary data (8857 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087664/SRX3087664.20_summits.bed INFO @ Sat, 17 Apr 2021 09:37:06: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (2658 records, 4 fields): 8 millis CompletedMACS2peakCalling