Job ID = 14519040 SRX = SRX7805907 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24954043 spots for SRR11185441/SRR11185441.sra Written 24954043 spots for SRR11185441/SRR11185441.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: 00:20:36 24954043 reads; of these: 24954043 (100.00%) were unpaired; of these: 2164948 (8.68%) aligned 0 times 16481955 (66.05%) aligned exactly 1 time 6307140 (25.28%) aligned >1 times 91.32% overall alignment rate Time searching: 00:20:37 Overall time: 00:20:37 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] 3871504 / 22789095 = 0.1699 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 14:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.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, 15 Jan 2022 14:46:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 14:46:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 14:46:42: 1000000 INFO @ Sat, 15 Jan 2022 14:46:53: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 14:47:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.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, 15 Jan 2022 14:47:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 14:47:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 14:47:04: 3000000 INFO @ Sat, 15 Jan 2022 14:47:11: 1000000 INFO @ Sat, 15 Jan 2022 14:47:15: 4000000 INFO @ Sat, 15 Jan 2022 14:47:20: 2000000 INFO @ Sat, 15 Jan 2022 14:47:26: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 14:47:31: 3000000 INFO @ Sat, 15 Jan 2022 14:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.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, 15 Jan 2022 14:47:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 14:47:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 14:47:38: 6000000 INFO @ Sat, 15 Jan 2022 14:47:41: 4000000 INFO @ Sat, 15 Jan 2022 14:47:43: 1000000 INFO @ Sat, 15 Jan 2022 14:47:49: 7000000 INFO @ Sat, 15 Jan 2022 14:47:50: 5000000 INFO @ Sat, 15 Jan 2022 14:47:55: 2000000 INFO @ Sat, 15 Jan 2022 14:48:00: 8000000 INFO @ Sat, 15 Jan 2022 14:48:00: 6000000 INFO @ Sat, 15 Jan 2022 14:48:07: 3000000 INFO @ Sat, 15 Jan 2022 14:48:10: 7000000 INFO @ Sat, 15 Jan 2022 14:48:11: 9000000 INFO @ Sat, 15 Jan 2022 14:48:18: 4000000 INFO @ Sat, 15 Jan 2022 14:48:20: 8000000 INFO @ Sat, 15 Jan 2022 14:48:21: 10000000 INFO @ Sat, 15 Jan 2022 14:48:29: 9000000 INFO @ Sat, 15 Jan 2022 14:48:30: 5000000 INFO @ Sat, 15 Jan 2022 14:48:31: 11000000 INFO @ Sat, 15 Jan 2022 14:48:38: 10000000 INFO @ Sat, 15 Jan 2022 14:48:41: 6000000 INFO @ Sat, 15 Jan 2022 14:48:42: 12000000 INFO @ Sat, 15 Jan 2022 14:48:47: 11000000 INFO @ Sat, 15 Jan 2022 14:48:53: 7000000 INFO @ Sat, 15 Jan 2022 14:48:54: 13000000 INFO @ Sat, 15 Jan 2022 14:48:56: 12000000 INFO @ Sat, 15 Jan 2022 14:49:04: 8000000 INFO @ Sat, 15 Jan 2022 14:49:05: 14000000 INFO @ Sat, 15 Jan 2022 14:49:06: 13000000 INFO @ Sat, 15 Jan 2022 14:49:15: 9000000 INFO @ Sat, 15 Jan 2022 14:49:15: 15000000 INFO @ Sat, 15 Jan 2022 14:49:17: 14000000 INFO @ Sat, 15 Jan 2022 14:49:26: 16000000 INFO @ Sat, 15 Jan 2022 14:49:26: 15000000 INFO @ Sat, 15 Jan 2022 14:49:26: 10000000 INFO @ Sat, 15 Jan 2022 14:49:35: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 14:49:37: 17000000 INFO @ Sat, 15 Jan 2022 14:49:38: 11000000 INFO @ Sat, 15 Jan 2022 14:49:45: 17000000 INFO @ Sat, 15 Jan 2022 14:49:48: 18000000 INFO @ Sat, 15 Jan 2022 14:49:49: 12000000 INFO @ Sat, 15 Jan 2022 14:49:54: 18000000 INFO @ Sat, 15 Jan 2022 14:49:58: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 14:49:58: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 14:49:58: #1 total tags in treatment: 18917591 INFO @ Sat, 15 Jan 2022 14:49:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 14:49:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 14:49:59: #1 tags after filtering in treatment: 18917476 INFO @ Sat, 15 Jan 2022 14:49:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 14:49:59: #1 finished! INFO @ Sat, 15 Jan 2022 14:49:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 14:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 14:50:00: 13000000 INFO @ Sat, 15 Jan 2022 14:50:01: #2 number of paired peaks: 9415 INFO @ Sat, 15 Jan 2022 14:50:01: start model_add_line... INFO @ Sat, 15 Jan 2022 14:50:01: start X-correlation... INFO @ Sat, 15 Jan 2022 14:50:02: end of X-cor INFO @ Sat, 15 Jan 2022 14:50:02: #2 finished! INFO @ Sat, 15 Jan 2022 14:50:02: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 14:50:02: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 15 Jan 2022 14:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.05_model.r WARNING @ Sat, 15 Jan 2022 14:50:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 14:50:02: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 15 Jan 2022 14:50:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 14:50:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 14:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 14:50:02: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 14:50:02: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 14:50:02: #1 total tags in treatment: 18917591 INFO @ Sat, 15 Jan 2022 14:50:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 14:50:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 14:50:03: #1 tags after filtering in treatment: 18917476 INFO @ Sat, 15 Jan 2022 14:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 14:50:03: #1 finished! INFO @ Sat, 15 Jan 2022 14:50:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 14:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 14:50:05: #2 number of paired peaks: 9415 INFO @ Sat, 15 Jan 2022 14:50:05: start model_add_line... INFO @ Sat, 15 Jan 2022 14:50:06: start X-correlation... INFO @ Sat, 15 Jan 2022 14:50:06: end of X-cor INFO @ Sat, 15 Jan 2022 14:50:06: #2 finished! INFO @ Sat, 15 Jan 2022 14:50:06: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 14:50:06: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 15 Jan 2022 14:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.10_model.r WARNING @ Sat, 15 Jan 2022 14:50:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 14:50:06: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 15 Jan 2022 14:50:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 14:50:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 14:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 14:50:11: 14000000 INFO @ Sat, 15 Jan 2022 14:50:22: 15000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 14:50:33: 16000000 INFO @ Sat, 15 Jan 2022 14:50:44: 17000000 INFO @ Sat, 15 Jan 2022 14:50:55: 18000000 INFO @ Sat, 15 Jan 2022 14:51:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 14:51:05: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 14:51:05: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 14:51:05: #1 total tags in treatment: 18917591 INFO @ Sat, 15 Jan 2022 14:51:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 14:51:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 14:51:05: #1 tags after filtering in treatment: 18917476 INFO @ Sat, 15 Jan 2022 14:51:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 14:51:05: #1 finished! INFO @ Sat, 15 Jan 2022 14:51:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 14:51:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 14:51:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 14:51:08: #2 number of paired peaks: 9415 INFO @ Sat, 15 Jan 2022 14:51:08: start model_add_line... INFO @ Sat, 15 Jan 2022 14:51:08: start X-correlation... INFO @ Sat, 15 Jan 2022 14:51:08: end of X-cor INFO @ Sat, 15 Jan 2022 14:51:08: #2 finished! INFO @ Sat, 15 Jan 2022 14:51:08: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 14:51:08: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 15 Jan 2022 14:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.20_model.r WARNING @ Sat, 15 Jan 2022 14:51:08: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 14:51:08: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 15 Jan 2022 14:51:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 14:51:08: #3 Call peaks... INFO @ Sat, 15 Jan 2022 14:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 14:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.05_peaks.xls INFO @ Sat, 15 Jan 2022 14:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 14:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.05_summits.bed INFO @ Sat, 15 Jan 2022 14:51:31: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (1547 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 14:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.10_peaks.xls INFO @ Sat, 15 Jan 2022 14:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 14:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.10_summits.bed INFO @ Sat, 15 Jan 2022 14:51:36: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (901 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 14:52:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 14:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.20_peaks.xls INFO @ Sat, 15 Jan 2022 14:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 14:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7805907/SRX7805907.20_summits.bed INFO @ Sat, 15 Jan 2022 14:52:38: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 5 millis CompletedMACS2peakCalling