Job ID = 12531438 SRX = SRX3087663 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 36421502 spots for SRR5927299/SRR5927299.sra Written 36421502 spots for SRR5927299/SRR5927299.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: 00:35:54 36421502 reads; of these: 36421502 (100.00%) were unpaired; of these: 3997532 (10.98%) aligned 0 times 23598128 (64.79%) aligned exactly 1 time 8825842 (24.23%) aligned >1 times 89.02% overall alignment rate Time searching: 00:35:59 Overall time: 00:35:59 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 16 files... [bam_rmdupse_core] 9934929 / 32423970 = 0.3064 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 08:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.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 08:07:55: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:07:55: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:08:00: 1000000 INFO @ Sat, 17 Apr 2021 08:08:06: 2000000 INFO @ Sat, 17 Apr 2021 08:08:12: 3000000 INFO @ Sat, 17 Apr 2021 08:08:17: 4000000 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 08:08:23: 5000000 INFO @ Sat, 17 Apr 2021 08:08:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.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 08:08:25: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:08:25: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:08:29: 6000000 INFO @ Sat, 17 Apr 2021 08:08:31: 1000000 INFO @ Sat, 17 Apr 2021 08:08:34: 7000000 INFO @ Sat, 17 Apr 2021 08:08:37: 2000000 INFO @ Sat, 17 Apr 2021 08:08:40: 8000000 INFO @ Sat, 17 Apr 2021 08:08:43: 3000000 INFO @ Sat, 17 Apr 2021 08:08:46: 9000000 INFO @ Sat, 17 Apr 2021 08:08:49: 4000000 INFO @ Sat, 17 Apr 2021 08:08:52: 10000000 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 08:08:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.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 08:08:55: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:08:55: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:08:55: 5000000 INFO @ Sat, 17 Apr 2021 08:08:58: 11000000 INFO @ Sat, 17 Apr 2021 08:09:01: 1000000 INFO @ Sat, 17 Apr 2021 08:09:01: 6000000 INFO @ Sat, 17 Apr 2021 08:09:04: 12000000 INFO @ Sat, 17 Apr 2021 08:09:07: 2000000 INFO @ Sat, 17 Apr 2021 08:09:07: 7000000 INFO @ Sat, 17 Apr 2021 08:09:10: 13000000 INFO @ Sat, 17 Apr 2021 08:09:13: 3000000 INFO @ Sat, 17 Apr 2021 08:09:13: 8000000 INFO @ Sat, 17 Apr 2021 08:09:16: 14000000 INFO @ Sat, 17 Apr 2021 08:09:19: 4000000 INFO @ Sat, 17 Apr 2021 08:09:19: 9000000 INFO @ Sat, 17 Apr 2021 08:09:22: 15000000 INFO @ Sat, 17 Apr 2021 08:09:25: 5000000 INFO @ Sat, 17 Apr 2021 08:09:25: 10000000 INFO @ Sat, 17 Apr 2021 08:09:28: 16000000 INFO @ Sat, 17 Apr 2021 08:09:31: 6000000 INFO @ Sat, 17 Apr 2021 08:09:31: 11000000 INFO @ Sat, 17 Apr 2021 08:09:34: 17000000 INFO @ Sat, 17 Apr 2021 08:09:37: 7000000 INFO @ Sat, 17 Apr 2021 08:09:37: 12000000 INFO @ Sat, 17 Apr 2021 08:09:40: 18000000 INFO @ Sat, 17 Apr 2021 08:09:43: 8000000 INFO @ Sat, 17 Apr 2021 08:09:43: 13000000 INFO @ Sat, 17 Apr 2021 08:09:46: 19000000 INFO @ Sat, 17 Apr 2021 08:09:49: 9000000 INFO @ Sat, 17 Apr 2021 08:09:49: 14000000 INFO @ Sat, 17 Apr 2021 08:09:52: 20000000 INFO @ Sat, 17 Apr 2021 08:09:55: 10000000 INFO @ Sat, 17 Apr 2021 08:09:55: 15000000 INFO @ Sat, 17 Apr 2021 08:09:58: 21000000 INFO @ Sat, 17 Apr 2021 08:10:01: 16000000 INFO @ Sat, 17 Apr 2021 08:10:02: 11000000 INFO @ Sat, 17 Apr 2021 08:10:04: 22000000 INFO @ Sat, 17 Apr 2021 08:10:07: 17000000 INFO @ Sat, 17 Apr 2021 08:10:08: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:10:08: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:10:08: #1 total tags in treatment: 22489041 INFO @ Sat, 17 Apr 2021 08:10:08: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:10:08: #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 08:10:08: #1 tags after filtering in treatment: 22488900 INFO @ Sat, 17 Apr 2021 08:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:10:08: #1 finished! INFO @ Sat, 17 Apr 2021 08:10:08: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:10:08: 12000000 INFO @ Sat, 17 Apr 2021 08:10:11: #2 number of paired peaks: 24376 INFO @ Sat, 17 Apr 2021 08:10:11: start model_add_line... INFO @ Sat, 17 Apr 2021 08:10:11: start X-correlation... INFO @ Sat, 17 Apr 2021 08:10:11: end of X-cor INFO @ Sat, 17 Apr 2021 08:10:11: #2 finished! INFO @ Sat, 17 Apr 2021 08:10:11: #2 predicted fragment length is 97 bps INFO @ Sat, 17 Apr 2021 08:10:11: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 17 Apr 2021 08:10:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.05_model.r WARNING @ Sat, 17 Apr 2021 08:10:11: #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 08:10:11: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 17 Apr 2021 08:10:11: #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 08:10:11: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:10:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:10:13: 18000000 INFO @ Sat, 17 Apr 2021 08:10:15: 13000000 INFO @ Sat, 17 Apr 2021 08:10:19: 19000000 INFO @ Sat, 17 Apr 2021 08:10:21: 14000000 INFO @ Sat, 17 Apr 2021 08:10:25: 20000000 INFO @ Sat, 17 Apr 2021 08:10:27: 15000000 INFO @ Sat, 17 Apr 2021 08:10:31: 21000000 INFO @ Sat, 17 Apr 2021 08:10:33: 16000000 INFO @ Sat, 17 Apr 2021 08:10:37: 22000000 INFO @ Sat, 17 Apr 2021 08:10:39: 17000000 INFO @ Sat, 17 Apr 2021 08:10:40: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:10:40: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:10:40: #1 total tags in treatment: 22489041 INFO @ Sat, 17 Apr 2021 08:10:40: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:10:40: #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 08:10:41: #1 tags after filtering in treatment: 22488900 INFO @ Sat, 17 Apr 2021 08:10:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:10:41: #1 finished! INFO @ Sat, 17 Apr 2021 08:10:41: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:10:44: #2 number of paired peaks: 24376 INFO @ Sat, 17 Apr 2021 08:10:44: start model_add_line... INFO @ Sat, 17 Apr 2021 08:10:44: start X-correlation... INFO @ Sat, 17 Apr 2021 08:10:44: end of X-cor INFO @ Sat, 17 Apr 2021 08:10:44: #2 finished! INFO @ Sat, 17 Apr 2021 08:10:44: #2 predicted fragment length is 97 bps INFO @ Sat, 17 Apr 2021 08:10:44: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 17 Apr 2021 08:10:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.10_model.r WARNING @ Sat, 17 Apr 2021 08:10:44: #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 08:10:44: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 17 Apr 2021 08:10:44: #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 08:10:44: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:10:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:10:45: 18000000 INFO @ Sat, 17 Apr 2021 08:10:50: 19000000 INFO @ Sat, 17 Apr 2021 08:10:56: 20000000 INFO @ Sat, 17 Apr 2021 08:11:02: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:11:08: 22000000 INFO @ Sat, 17 Apr 2021 08:11:10: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:11:11: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:11:11: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:11:11: #1 total tags in treatment: 22489041 INFO @ Sat, 17 Apr 2021 08:11:11: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:11:11: #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 08:11:11: #1 tags after filtering in treatment: 22488900 INFO @ Sat, 17 Apr 2021 08:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:11:11: #1 finished! INFO @ Sat, 17 Apr 2021 08:11:11: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:11:14: #2 number of paired peaks: 24376 INFO @ Sat, 17 Apr 2021 08:11:14: start model_add_line... INFO @ Sat, 17 Apr 2021 08:11:14: start X-correlation... INFO @ Sat, 17 Apr 2021 08:11:14: end of X-cor INFO @ Sat, 17 Apr 2021 08:11:14: #2 finished! INFO @ Sat, 17 Apr 2021 08:11:14: #2 predicted fragment length is 97 bps INFO @ Sat, 17 Apr 2021 08:11:14: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 17 Apr 2021 08:11:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.20_model.r WARNING @ Sat, 17 Apr 2021 08:11:14: #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 08:11:14: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 17 Apr 2021 08:11:14: #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 08:11:14: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:11:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.05_summits.bed INFO @ Sat, 17 Apr 2021 08:11:41: Done! pass1 - making usageList (87 chroms): 3 millis pass2 - checking and writing primary data (15123 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:11:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:12:11: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.10_summits.bed INFO @ Sat, 17 Apr 2021 08:12:14: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (5587 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087663/SRX3087663.20_summits.bed INFO @ Sat, 17 Apr 2021 08:12:41: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (1204 records, 4 fields): 4 millis CompletedMACS2peakCalling