Job ID = 8184617 SRX = SRX8047627 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:58:28 prefetch.2.10.7: 1) Downloading 'SRR11471351'... 2020-08-10T04:58:28 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:59:28 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:59:28 prefetch.2.10.7: 1) 'SRR11471351' was downloaded successfully Read 21608929 spots for SRR11471351/SRR11471351.sra Written 21608929 spots for SRR11471351/SRR11471351.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: 00:18:56 21608929 reads; of these: 21608929 (100.00%) were unpaired; of these: 579109 (2.68%) aligned 0 times 15007802 (69.45%) aligned exactly 1 time 6022018 (27.87%) aligned >1 times 97.32% overall alignment rate Time searching: 00:18:57 Overall time: 00:18:57 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] 736348 / 21029820 = 0.0350 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 10 Aug 2020 14:25:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.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 @ Mon, 10 Aug 2020 14:25:29: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:25:29: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:25:34: 1000000 INFO @ Mon, 10 Aug 2020 14:25:39: 2000000 INFO @ Mon, 10 Aug 2020 14:25:44: 3000000 INFO @ Mon, 10 Aug 2020 14:25:49: 4000000 INFO @ Mon, 10 Aug 2020 14:25:54: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 10 Aug 2020 14:25:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.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 @ Mon, 10 Aug 2020 14:25:59: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:25:59: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:25:59: 6000000 INFO @ Mon, 10 Aug 2020 14:26:04: 7000000 INFO @ Mon, 10 Aug 2020 14:26:04: 1000000 INFO @ Mon, 10 Aug 2020 14:26:09: 8000000 INFO @ Mon, 10 Aug 2020 14:26:09: 2000000 INFO @ Mon, 10 Aug 2020 14:26:14: 9000000 INFO @ Mon, 10 Aug 2020 14:26:14: 3000000 INFO @ Mon, 10 Aug 2020 14:26:20: 10000000 INFO @ Mon, 10 Aug 2020 14:26:20: 4000000 INFO @ Mon, 10 Aug 2020 14:26:25: 11000000 INFO @ Mon, 10 Aug 2020 14:26:25: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 10 Aug 2020 14:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.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 @ Mon, 10 Aug 2020 14:26:29: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:26:29: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:26:30: 12000000 INFO @ Mon, 10 Aug 2020 14:26:30: 6000000 INFO @ Mon, 10 Aug 2020 14:26:34: 1000000 INFO @ Mon, 10 Aug 2020 14:26:35: 13000000 INFO @ Mon, 10 Aug 2020 14:26:35: 7000000 INFO @ Mon, 10 Aug 2020 14:26:39: 2000000 INFO @ Mon, 10 Aug 2020 14:26:40: 14000000 INFO @ Mon, 10 Aug 2020 14:26:40: 8000000 INFO @ Mon, 10 Aug 2020 14:26:45: 3000000 INFO @ Mon, 10 Aug 2020 14:26:45: 15000000 INFO @ Mon, 10 Aug 2020 14:26:46: 9000000 INFO @ Mon, 10 Aug 2020 14:26:50: 4000000 INFO @ Mon, 10 Aug 2020 14:26:51: 16000000 INFO @ Mon, 10 Aug 2020 14:26:51: 10000000 INFO @ Mon, 10 Aug 2020 14:26:55: 5000000 INFO @ Mon, 10 Aug 2020 14:26:56: 17000000 INFO @ Mon, 10 Aug 2020 14:26:56: 11000000 INFO @ Mon, 10 Aug 2020 14:27:00: 6000000 INFO @ Mon, 10 Aug 2020 14:27:01: 12000000 INFO @ Mon, 10 Aug 2020 14:27:01: 18000000 INFO @ Mon, 10 Aug 2020 14:27:05: 7000000 INFO @ Mon, 10 Aug 2020 14:27:06: 13000000 INFO @ Mon, 10 Aug 2020 14:27:06: 19000000 INFO @ Mon, 10 Aug 2020 14:27:11: 8000000 INFO @ Mon, 10 Aug 2020 14:27:11: 14000000 INFO @ Mon, 10 Aug 2020 14:27:12: 20000000 INFO @ Mon, 10 Aug 2020 14:27:13: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:27:13: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:27:13: #1 total tags in treatment: 20293472 INFO @ Mon, 10 Aug 2020 14:27:13: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:27:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:27:14: #1 tags after filtering in treatment: 20293352 INFO @ Mon, 10 Aug 2020 14:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:27:14: #1 finished! INFO @ Mon, 10 Aug 2020 14:27:14: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:27:16: #2 number of paired peaks: 7201 INFO @ Mon, 10 Aug 2020 14:27:16: start model_add_line... INFO @ Mon, 10 Aug 2020 14:27:16: 9000000 INFO @ Mon, 10 Aug 2020 14:27:16: start X-correlation... INFO @ Mon, 10 Aug 2020 14:27:16: end of X-cor INFO @ Mon, 10 Aug 2020 14:27:16: #2 finished! INFO @ Mon, 10 Aug 2020 14:27:16: #2 predicted fragment length is 51 bps INFO @ Mon, 10 Aug 2020 14:27:16: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 10 Aug 2020 14:27:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.05_model.r WARNING @ Mon, 10 Aug 2020 14:27:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:27:16: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 10 Aug 2020 14:27:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:27:16: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:27:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:27:17: 15000000 INFO @ Mon, 10 Aug 2020 14:27:21: 10000000 INFO @ Mon, 10 Aug 2020 14:27:22: 16000000 INFO @ Mon, 10 Aug 2020 14:27:26: 11000000 INFO @ Mon, 10 Aug 2020 14:27:27: 17000000 INFO @ Mon, 10 Aug 2020 14:27:31: 12000000 INFO @ Mon, 10 Aug 2020 14:27:32: 18000000 INFO @ Mon, 10 Aug 2020 14:27:37: 13000000 INFO @ Mon, 10 Aug 2020 14:27:38: 19000000 INFO @ Mon, 10 Aug 2020 14:27:42: 14000000 INFO @ Mon, 10 Aug 2020 14:27:43: 20000000 INFO @ Mon, 10 Aug 2020 14:27:45: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:27:45: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:27:45: #1 total tags in treatment: 20293472 INFO @ Mon, 10 Aug 2020 14:27:45: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:27:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:27:45: #1 tags after filtering in treatment: 20293352 INFO @ Mon, 10 Aug 2020 14:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:27:45: #1 finished! INFO @ Mon, 10 Aug 2020 14:27:45: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:27:47: 15000000 INFO @ Mon, 10 Aug 2020 14:27:47: #2 number of paired peaks: 7201 INFO @ Mon, 10 Aug 2020 14:27:47: start model_add_line... INFO @ Mon, 10 Aug 2020 14:27:47: start X-correlation... INFO @ Mon, 10 Aug 2020 14:27:47: end of X-cor INFO @ Mon, 10 Aug 2020 14:27:47: #2 finished! INFO @ Mon, 10 Aug 2020 14:27:47: #2 predicted fragment length is 51 bps INFO @ Mon, 10 Aug 2020 14:27:47: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 10 Aug 2020 14:27:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.10_model.r WARNING @ Mon, 10 Aug 2020 14:27:47: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:27:47: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 10 Aug 2020 14:27:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:27:47: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:27:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:27:52: 16000000 INFO @ Mon, 10 Aug 2020 14:27:57: 17000000 INFO @ Mon, 10 Aug 2020 14:28:00: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:28:02: 18000000 INFO @ Mon, 10 Aug 2020 14:28:07: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:28:12: 20000000 INFO @ Mon, 10 Aug 2020 14:28:14: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:28:14: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:28:14: #1 total tags in treatment: 20293472 INFO @ Mon, 10 Aug 2020 14:28:14: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:28:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:28:14: #1 tags after filtering in treatment: 20293352 INFO @ Mon, 10 Aug 2020 14:28:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:28:14: #1 finished! INFO @ Mon, 10 Aug 2020 14:28:14: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:28:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:28:16: #2 number of paired peaks: 7201 INFO @ Mon, 10 Aug 2020 14:28:16: start model_add_line... INFO @ Mon, 10 Aug 2020 14:28:16: start X-correlation... INFO @ Mon, 10 Aug 2020 14:28:16: end of X-cor INFO @ Mon, 10 Aug 2020 14:28:16: #2 finished! INFO @ Mon, 10 Aug 2020 14:28:16: #2 predicted fragment length is 51 bps INFO @ Mon, 10 Aug 2020 14:28:16: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 10 Aug 2020 14:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.20_model.r WARNING @ Mon, 10 Aug 2020 14:28:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:28:16: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 10 Aug 2020 14:28:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:28:16: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:28:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.05_summits.bed INFO @ Mon, 10 Aug 2020 14:28:22: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (2698 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:28:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.10_summits.bed INFO @ Mon, 10 Aug 2020 14:28:55: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (1170 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:29:01: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:29:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:29:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:29:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047627/SRX8047627.20_summits.bed INFO @ Mon, 10 Aug 2020 14:29:23: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 3 millis CompletedMACS2peakCalling