Job ID = 8184448 SRX = SRX8047593 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:20:46 prefetch.2.10.7: 1) Downloading 'SRR11471317'... 2020-08-10T03:20:46 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:21:34 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:21:34 prefetch.2.10.7: 1) 'SRR11471317' was downloaded successfully Read 15825202 spots for SRR11471317/SRR11471317.sra Written 15825202 spots for SRR11471317/SRR11471317.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:37:11 15825202 reads; of these: 15825202 (100.00%) were unpaired; of these: 856251 (5.41%) aligned 0 times 7516618 (47.50%) aligned exactly 1 time 7452333 (47.09%) aligned >1 times 94.59% overall alignment rate Time searching: 00:37:13 Overall time: 00:37:13 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 8 files... [bam_rmdupse_core] 1534792 / 14968951 = 0.1025 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 13:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.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 13:04:04: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:04:04: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:04:12: 1000000 INFO @ Mon, 10 Aug 2020 13:04:19: 2000000 INFO @ Mon, 10 Aug 2020 13:04:27: 3000000 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 13:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.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 13:04:34: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:04:34: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:04:34: 4000000 INFO @ Mon, 10 Aug 2020 13:04:42: 1000000 INFO @ Mon, 10 Aug 2020 13:04:43: 5000000 INFO @ Mon, 10 Aug 2020 13:04:50: 2000000 INFO @ Mon, 10 Aug 2020 13:04:51: 6000000 INFO @ Mon, 10 Aug 2020 13:04:59: 3000000 INFO @ Mon, 10 Aug 2020 13:04:59: 7000000 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 13:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.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 13:05:04: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:05:04: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:05:07: 4000000 INFO @ Mon, 10 Aug 2020 13:05:07: 8000000 INFO @ Mon, 10 Aug 2020 13:05:12: 1000000 INFO @ Mon, 10 Aug 2020 13:05:15: 5000000 INFO @ Mon, 10 Aug 2020 13:05:15: 9000000 INFO @ Mon, 10 Aug 2020 13:05:21: 2000000 INFO @ Mon, 10 Aug 2020 13:05:24: 6000000 INFO @ Mon, 10 Aug 2020 13:05:24: 10000000 INFO @ Mon, 10 Aug 2020 13:05:29: 3000000 INFO @ Mon, 10 Aug 2020 13:05:32: 7000000 INFO @ Mon, 10 Aug 2020 13:05:33: 11000000 INFO @ Mon, 10 Aug 2020 13:05:38: 4000000 INFO @ Mon, 10 Aug 2020 13:05:41: 8000000 INFO @ Mon, 10 Aug 2020 13:05:41: 12000000 INFO @ Mon, 10 Aug 2020 13:05:46: 5000000 INFO @ Mon, 10 Aug 2020 13:05:49: 9000000 INFO @ Mon, 10 Aug 2020 13:05:50: 13000000 INFO @ Mon, 10 Aug 2020 13:05:53: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:05:53: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:05:53: #1 total tags in treatment: 13434159 INFO @ Mon, 10 Aug 2020 13:05:53: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:05:53: #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 13:05:54: #1 tags after filtering in treatment: 13434005 INFO @ Mon, 10 Aug 2020 13:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:05:54: #1 finished! INFO @ Mon, 10 Aug 2020 13:05:54: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:05:55: 6000000 INFO @ Mon, 10 Aug 2020 13:05:56: #2 number of paired peaks: 32943 INFO @ Mon, 10 Aug 2020 13:05:56: start model_add_line... INFO @ Mon, 10 Aug 2020 13:05:56: start X-correlation... INFO @ Mon, 10 Aug 2020 13:05:56: end of X-cor INFO @ Mon, 10 Aug 2020 13:05:56: #2 finished! INFO @ Mon, 10 Aug 2020 13:05:56: #2 predicted fragment length is 55 bps INFO @ Mon, 10 Aug 2020 13:05:56: #2 alternative fragment length(s) may be 55 bps INFO @ Mon, 10 Aug 2020 13:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.05_model.r WARNING @ Mon, 10 Aug 2020 13:05:56: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:05:56: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Mon, 10 Aug 2020 13:05:56: #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 13:05:56: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:05:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:05:58: 10000000 INFO @ Mon, 10 Aug 2020 13:06:03: 7000000 INFO @ Mon, 10 Aug 2020 13:06:06: 11000000 INFO @ Mon, 10 Aug 2020 13:06:11: 8000000 INFO @ Mon, 10 Aug 2020 13:06:14: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:06:19: 9000000 INFO @ Mon, 10 Aug 2020 13:06:23: 13000000 INFO @ Mon, 10 Aug 2020 13:06:26: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:06:26: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:06:26: #1 total tags in treatment: 13434159 INFO @ Mon, 10 Aug 2020 13:06:26: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:06:26: #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 13:06:27: #1 tags after filtering in treatment: 13434005 INFO @ Mon, 10 Aug 2020 13:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:06:27: #1 finished! INFO @ Mon, 10 Aug 2020 13:06:27: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:06:27: 10000000 INFO @ Mon, 10 Aug 2020 13:06:29: #2 number of paired peaks: 32943 INFO @ Mon, 10 Aug 2020 13:06:29: start model_add_line... INFO @ Mon, 10 Aug 2020 13:06:29: start X-correlation... INFO @ Mon, 10 Aug 2020 13:06:29: end of X-cor INFO @ Mon, 10 Aug 2020 13:06:29: #2 finished! INFO @ Mon, 10 Aug 2020 13:06:29: #2 predicted fragment length is 55 bps INFO @ Mon, 10 Aug 2020 13:06:29: #2 alternative fragment length(s) may be 55 bps INFO @ Mon, 10 Aug 2020 13:06:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.10_model.r WARNING @ Mon, 10 Aug 2020 13:06:29: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:06:29: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Mon, 10 Aug 2020 13:06:29: #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 13:06:29: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:06:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:06:30: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:06:35: 11000000 INFO @ Mon, 10 Aug 2020 13:06:43: 12000000 BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:06:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.05_summits.bed INFO @ Mon, 10 Aug 2020 13:06:47: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (5112 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:06:50: 13000000 INFO @ Mon, 10 Aug 2020 13:06:53: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:06:53: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:06:53: #1 total tags in treatment: 13434159 INFO @ Mon, 10 Aug 2020 13:06:53: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:06:53: #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 13:06:54: #1 tags after filtering in treatment: 13434005 INFO @ Mon, 10 Aug 2020 13:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:06:54: #1 finished! INFO @ Mon, 10 Aug 2020 13:06:54: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:06:56: #2 number of paired peaks: 32943 INFO @ Mon, 10 Aug 2020 13:06:56: start model_add_line... INFO @ Mon, 10 Aug 2020 13:06:56: start X-correlation... INFO @ Mon, 10 Aug 2020 13:06:56: end of X-cor INFO @ Mon, 10 Aug 2020 13:06:56: #2 finished! INFO @ Mon, 10 Aug 2020 13:06:56: #2 predicted fragment length is 55 bps INFO @ Mon, 10 Aug 2020 13:06:56: #2 alternative fragment length(s) may be 55 bps INFO @ Mon, 10 Aug 2020 13:06:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.20_model.r WARNING @ Mon, 10 Aug 2020 13:06:56: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:06:56: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Mon, 10 Aug 2020 13:06:56: #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 13:06:56: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:06:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:07:01: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.10_summits.bed INFO @ Mon, 10 Aug 2020 13:07:18: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1711 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:07:28: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047593/SRX8047593.20_summits.bed INFO @ Mon, 10 Aug 2020 13:07:45: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (604 records, 4 fields): 3 millis CompletedMACS2peakCalling