Job ID = 14518179 SRX = SRX9430847 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 40146967 spots for SRR12979020/SRR12979020.sra Written 40146967 spots for SRR12979020/SRR12979020.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: 00:28:04 40146967 reads; of these: 40146967 (100.00%) were unpaired; of these: 922307 (2.30%) aligned 0 times 28238104 (70.34%) aligned exactly 1 time 10986556 (27.37%) aligned >1 times 97.70% overall alignment rate Time searching: 00:28:05 Overall time: 00:28:05 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] 1111193 / 39224660 = 0.0283 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 11:25:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.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 11:25:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:25:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:25:35: 1000000 INFO @ Sat, 15 Jan 2022 11:25:41: 2000000 INFO @ Sat, 15 Jan 2022 11:25:46: 3000000 INFO @ Sat, 15 Jan 2022 11:25:52: 4000000 INFO @ Sat, 15 Jan 2022 11:25:58: 5000000 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 11:25:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.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 11:25:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:25:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:26:04: 6000000 INFO @ Sat, 15 Jan 2022 11:26:07: 1000000 INFO @ Sat, 15 Jan 2022 11:26:11: 7000000 INFO @ Sat, 15 Jan 2022 11:26:14: 2000000 INFO @ Sat, 15 Jan 2022 11:26:17: 8000000 INFO @ Sat, 15 Jan 2022 11:26:21: 3000000 INFO @ Sat, 15 Jan 2022 11:26:24: 9000000 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 11:26:28: 4000000 INFO @ Sat, 15 Jan 2022 11:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.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 11:26:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:26:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:26:30: 10000000 INFO @ Sat, 15 Jan 2022 11:26:35: 5000000 INFO @ Sat, 15 Jan 2022 11:26:37: 11000000 INFO @ Sat, 15 Jan 2022 11:26:37: 1000000 INFO @ Sat, 15 Jan 2022 11:26:43: 6000000 INFO @ Sat, 15 Jan 2022 11:26:43: 12000000 INFO @ Sat, 15 Jan 2022 11:26:44: 2000000 INFO @ Sat, 15 Jan 2022 11:26:50: 13000000 INFO @ Sat, 15 Jan 2022 11:26:50: 7000000 INFO @ Sat, 15 Jan 2022 11:26:52: 3000000 INFO @ Sat, 15 Jan 2022 11:26:57: 14000000 INFO @ Sat, 15 Jan 2022 11:26:58: 8000000 INFO @ Sat, 15 Jan 2022 11:26:59: 4000000 INFO @ Sat, 15 Jan 2022 11:27:03: 15000000 INFO @ Sat, 15 Jan 2022 11:27:05: 9000000 INFO @ Sat, 15 Jan 2022 11:27:06: 5000000 INFO @ Sat, 15 Jan 2022 11:27:10: 16000000 INFO @ Sat, 15 Jan 2022 11:27:12: 10000000 INFO @ Sat, 15 Jan 2022 11:27:13: 6000000 INFO @ Sat, 15 Jan 2022 11:27:17: 17000000 INFO @ Sat, 15 Jan 2022 11:27:19: 11000000 INFO @ Sat, 15 Jan 2022 11:27:20: 7000000 INFO @ Sat, 15 Jan 2022 11:27:24: 18000000 INFO @ Sat, 15 Jan 2022 11:27:26: 12000000 INFO @ Sat, 15 Jan 2022 11:27:28: 8000000 INFO @ Sat, 15 Jan 2022 11:27:31: 19000000 INFO @ Sat, 15 Jan 2022 11:27:33: 13000000 INFO @ Sat, 15 Jan 2022 11:27:35: 9000000 INFO @ Sat, 15 Jan 2022 11:27:37: 20000000 INFO @ Sat, 15 Jan 2022 11:27:41: 14000000 INFO @ Sat, 15 Jan 2022 11:27:42: 10000000 INFO @ Sat, 15 Jan 2022 11:27:44: 21000000 INFO @ Sat, 15 Jan 2022 11:27:48: 15000000 INFO @ Sat, 15 Jan 2022 11:27:49: 11000000 INFO @ Sat, 15 Jan 2022 11:27:51: 22000000 INFO @ Sat, 15 Jan 2022 11:27:55: 16000000 INFO @ Sat, 15 Jan 2022 11:27:56: 12000000 INFO @ Sat, 15 Jan 2022 11:27:57: 23000000 INFO @ Sat, 15 Jan 2022 11:28:02: 17000000 INFO @ Sat, 15 Jan 2022 11:28:03: 13000000 INFO @ Sat, 15 Jan 2022 11:28:04: 24000000 INFO @ Sat, 15 Jan 2022 11:28:10: 18000000 INFO @ Sat, 15 Jan 2022 11:28:10: 14000000 INFO @ Sat, 15 Jan 2022 11:28:11: 25000000 INFO @ Sat, 15 Jan 2022 11:28:17: 19000000 INFO @ Sat, 15 Jan 2022 11:28:17: 15000000 INFO @ Sat, 15 Jan 2022 11:28:17: 26000000 INFO @ Sat, 15 Jan 2022 11:28:24: 20000000 INFO @ Sat, 15 Jan 2022 11:28:24: 27000000 INFO @ Sat, 15 Jan 2022 11:28:24: 16000000 INFO @ Sat, 15 Jan 2022 11:28:31: 28000000 INFO @ Sat, 15 Jan 2022 11:28:31: 21000000 INFO @ Sat, 15 Jan 2022 11:28:32: 17000000 INFO @ Sat, 15 Jan 2022 11:28:37: 29000000 INFO @ Sat, 15 Jan 2022 11:28:38: 22000000 INFO @ Sat, 15 Jan 2022 11:28:39: 18000000 INFO @ Sat, 15 Jan 2022 11:28:44: 30000000 INFO @ Sat, 15 Jan 2022 11:28:46: 23000000 INFO @ Sat, 15 Jan 2022 11:28:47: 19000000 INFO @ Sat, 15 Jan 2022 11:28:50: 31000000 INFO @ Sat, 15 Jan 2022 11:28:53: 24000000 INFO @ Sat, 15 Jan 2022 11:28:54: 20000000 INFO @ Sat, 15 Jan 2022 11:28:57: 32000000 INFO @ Sat, 15 Jan 2022 11:29:00: 25000000 INFO @ Sat, 15 Jan 2022 11:29:01: 21000000 INFO @ Sat, 15 Jan 2022 11:29:04: 33000000 INFO @ Sat, 15 Jan 2022 11:29:07: 26000000 INFO @ Sat, 15 Jan 2022 11:29:08: 22000000 INFO @ Sat, 15 Jan 2022 11:29:11: 34000000 INFO @ Sat, 15 Jan 2022 11:29:14: 27000000 INFO @ Sat, 15 Jan 2022 11:29:15: 23000000 INFO @ Sat, 15 Jan 2022 11:29:17: 35000000 INFO @ Sat, 15 Jan 2022 11:29:22: 28000000 INFO @ Sat, 15 Jan 2022 11:29:22: 24000000 INFO @ Sat, 15 Jan 2022 11:29:24: 36000000 INFO @ Sat, 15 Jan 2022 11:29:29: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 11:29:30: 25000000 INFO @ Sat, 15 Jan 2022 11:29:31: 37000000 INFO @ Sat, 15 Jan 2022 11:29:36: 30000000 INFO @ Sat, 15 Jan 2022 11:29:37: 26000000 INFO @ Sat, 15 Jan 2022 11:29:38: 38000000 INFO @ Sat, 15 Jan 2022 11:29:39: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 11:29:39: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 11:29:39: #1 total tags in treatment: 38113467 INFO @ Sat, 15 Jan 2022 11:29:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:29:39: #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 11:29:39: #1 tags after filtering in treatment: 38113403 INFO @ Sat, 15 Jan 2022 11:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:29:39: #1 finished! INFO @ Sat, 15 Jan 2022 11:29:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:29:43: #2 number of paired peaks: 4519 INFO @ Sat, 15 Jan 2022 11:29:43: start model_add_line... INFO @ Sat, 15 Jan 2022 11:29:43: start X-correlation... INFO @ Sat, 15 Jan 2022 11:29:43: end of X-cor INFO @ Sat, 15 Jan 2022 11:29:43: #2 finished! INFO @ Sat, 15 Jan 2022 11:29:43: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 11:29:43: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 15 Jan 2022 11:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.05_model.r WARNING @ Sat, 15 Jan 2022 11:29:43: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 11:29:43: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 15 Jan 2022 11:29:43: #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 11:29:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:29:43: 31000000 INFO @ Sat, 15 Jan 2022 11:29:43: 27000000 INFO @ Sat, 15 Jan 2022 11:29:50: 28000000 INFO @ Sat, 15 Jan 2022 11:29:50: 32000000 INFO @ Sat, 15 Jan 2022 11:29:56: 29000000 INFO @ Sat, 15 Jan 2022 11:29:57: 33000000 INFO @ Sat, 15 Jan 2022 11:30:03: 30000000 INFO @ Sat, 15 Jan 2022 11:30:05: 34000000 INFO @ Sat, 15 Jan 2022 11:30:09: 31000000 INFO @ Sat, 15 Jan 2022 11:30:12: 35000000 INFO @ Sat, 15 Jan 2022 11:30:16: 32000000 INFO @ Sat, 15 Jan 2022 11:30:19: 36000000 INFO @ Sat, 15 Jan 2022 11:30:22: 33000000 INFO @ Sat, 15 Jan 2022 11:30:26: 37000000 INFO @ Sat, 15 Jan 2022 11:30:29: 34000000 INFO @ Sat, 15 Jan 2022 11:30:33: 38000000 INFO @ Sat, 15 Jan 2022 11:30:34: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 11:30:34: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 11:30:34: #1 total tags in treatment: 38113467 INFO @ Sat, 15 Jan 2022 11:30:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:30:34: #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 11:30:35: #1 tags after filtering in treatment: 38113403 INFO @ Sat, 15 Jan 2022 11:30:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:30:35: #1 finished! INFO @ Sat, 15 Jan 2022 11:30:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:30:35: 35000000 INFO @ Sat, 15 Jan 2022 11:30:38: #2 number of paired peaks: 4519 INFO @ Sat, 15 Jan 2022 11:30:38: start model_add_line... INFO @ Sat, 15 Jan 2022 11:30:38: start X-correlation... INFO @ Sat, 15 Jan 2022 11:30:38: end of X-cor INFO @ Sat, 15 Jan 2022 11:30:38: #2 finished! INFO @ Sat, 15 Jan 2022 11:30:38: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 11:30:38: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 15 Jan 2022 11:30:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.10_model.r WARNING @ Sat, 15 Jan 2022 11:30:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 11:30:38: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 15 Jan 2022 11:30:38: #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 11:30:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:30:42: 36000000 INFO @ Sat, 15 Jan 2022 11:30:48: 37000000 INFO @ Sat, 15 Jan 2022 11:30:53: 38000000 INFO @ Sat, 15 Jan 2022 11:30:54: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 11:30:54: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 11:30:54: #1 total tags in treatment: 38113467 INFO @ Sat, 15 Jan 2022 11:30:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:30:54: #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 11:30:55: #1 tags after filtering in treatment: 38113403 INFO @ Sat, 15 Jan 2022 11:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:30:55: #1 finished! INFO @ Sat, 15 Jan 2022 11:30:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:30:55: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 11:30:58: #2 number of paired peaks: 4519 INFO @ Sat, 15 Jan 2022 11:30:58: start model_add_line... INFO @ Sat, 15 Jan 2022 11:30:58: start X-correlation... INFO @ Sat, 15 Jan 2022 11:30:58: end of X-cor INFO @ Sat, 15 Jan 2022 11:30:58: #2 finished! INFO @ Sat, 15 Jan 2022 11:30:58: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 11:30:58: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 15 Jan 2022 11:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.20_model.r WARNING @ Sat, 15 Jan 2022 11:30:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 11:30:58: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 15 Jan 2022 11:30:58: #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 11:30:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:31:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:31:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.05_peaks.xls INFO @ Sat, 15 Jan 2022 11:31:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:31:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.05_summits.bed INFO @ Sat, 15 Jan 2022 11:31:46: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (1929 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:31:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:32:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.10_peaks.xls INFO @ Sat, 15 Jan 2022 11:32:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:32:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.10_summits.bed INFO @ Sat, 15 Jan 2022 11:32:40: Done! pass1 - making usageList (43 chroms): 0 millis pass2 - checking and writing primary data (1133 records, 4 fields): 293 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.20_peaks.xls INFO @ Sat, 15 Jan 2022 11:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430847/SRX9430847.20_summits.bed INFO @ Sat, 15 Jan 2022 11:33:01: Done! pass1 - making usageList (35 chroms): 0 millis pass2 - checking and writing primary data (569 records, 4 fields): 10 millis CompletedMACS2peakCalling