Job ID = 8184606 SRX = SRX8047620 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:53:23 prefetch.2.10.7: 1) Downloading 'SRR11471344'... 2020-08-10T04:53:23 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:54:02 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:54:03 prefetch.2.10.7: 'SRR11471344' is valid 2020-08-10T04:54:03 prefetch.2.10.7: 1) 'SRR11471344' was downloaded successfully Read 12376392 spots for SRR11471344/SRR11471344.sra Written 12376392 spots for SRR11471344/SRR11471344.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:10:51 12376392 reads; of these: 12376392 (100.00%) were unpaired; of these: 334432 (2.70%) aligned 0 times 8629325 (69.72%) aligned exactly 1 time 3412635 (27.57%) aligned >1 times 97.30% overall alignment rate Time searching: 00:10:54 Overall time: 00:10:54 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] 676126 / 12041960 = 0.0561 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 14:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.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 14:09:18: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:09:18: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:09:23: 1000000 INFO @ Mon, 10 Aug 2020 14:09:29: 2000000 INFO @ Mon, 10 Aug 2020 14:09:35: 3000000 INFO @ Mon, 10 Aug 2020 14:09:41: 4000000 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 14:09:47: 5000000 INFO @ Mon, 10 Aug 2020 14:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.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 14:09:47: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:09:47: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:09:54: 6000000 INFO @ Mon, 10 Aug 2020 14:09:54: 1000000 INFO @ Mon, 10 Aug 2020 14:10:00: 7000000 INFO @ Mon, 10 Aug 2020 14:10:01: 2000000 INFO @ Mon, 10 Aug 2020 14:10:07: 8000000 INFO @ Mon, 10 Aug 2020 14:10:07: 3000000 INFO @ Mon, 10 Aug 2020 14:10:13: 9000000 INFO @ Mon, 10 Aug 2020 14:10:14: 4000000 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 14:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.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 14:10:18: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:10:18: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:10:20: 10000000 INFO @ Mon, 10 Aug 2020 14:10:21: 5000000 INFO @ Mon, 10 Aug 2020 14:10:24: 1000000 INFO @ Mon, 10 Aug 2020 14:10:27: 11000000 INFO @ Mon, 10 Aug 2020 14:10:27: 6000000 INFO @ Mon, 10 Aug 2020 14:10:29: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:10:29: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:10:29: #1 total tags in treatment: 11365834 INFO @ Mon, 10 Aug 2020 14:10:29: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:10:29: #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 14:10:29: #1 tags after filtering in treatment: 11365661 INFO @ Mon, 10 Aug 2020 14:10:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:10:29: #1 finished! INFO @ Mon, 10 Aug 2020 14:10:29: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:10:31: #2 number of paired peaks: 6205 INFO @ Mon, 10 Aug 2020 14:10:31: start model_add_line... INFO @ Mon, 10 Aug 2020 14:10:31: start X-correlation... INFO @ Mon, 10 Aug 2020 14:10:31: end of X-cor INFO @ Mon, 10 Aug 2020 14:10:31: #2 finished! INFO @ Mon, 10 Aug 2020 14:10:31: #2 predicted fragment length is 51 bps INFO @ Mon, 10 Aug 2020 14:10:31: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 10 Aug 2020 14:10:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.05_model.r WARNING @ Mon, 10 Aug 2020 14:10:31: #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 14:10:31: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 10 Aug 2020 14:10:31: #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 14:10:31: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:10:31: 2000000 INFO @ Mon, 10 Aug 2020 14:10:34: 7000000 INFO @ Mon, 10 Aug 2020 14:10:37: 3000000 INFO @ Mon, 10 Aug 2020 14:10:40: 8000000 INFO @ Mon, 10 Aug 2020 14:10:43: 4000000 INFO @ Mon, 10 Aug 2020 14:10:46: 9000000 INFO @ Mon, 10 Aug 2020 14:10:49: 5000000 INFO @ Mon, 10 Aug 2020 14:10:52: 10000000 INFO @ Mon, 10 Aug 2020 14:10:56: 6000000 INFO @ Mon, 10 Aug 2020 14:10:56: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:10:58: 11000000 INFO @ Mon, 10 Aug 2020 14:11:01: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:11:01: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:11:01: #1 total tags in treatment: 11365834 INFO @ Mon, 10 Aug 2020 14:11:01: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:11:01: #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 14:11:01: #1 tags after filtering in treatment: 11365661 INFO @ Mon, 10 Aug 2020 14:11:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:11:01: #1 finished! INFO @ Mon, 10 Aug 2020 14:11:01: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:11:02: 7000000 INFO @ Mon, 10 Aug 2020 14:11:02: #2 number of paired peaks: 6205 INFO @ Mon, 10 Aug 2020 14:11:02: start model_add_line... INFO @ Mon, 10 Aug 2020 14:11:02: start X-correlation... INFO @ Mon, 10 Aug 2020 14:11:02: end of X-cor INFO @ Mon, 10 Aug 2020 14:11:02: #2 finished! INFO @ Mon, 10 Aug 2020 14:11:02: #2 predicted fragment length is 51 bps INFO @ Mon, 10 Aug 2020 14:11:02: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 10 Aug 2020 14:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.10_model.r WARNING @ Mon, 10 Aug 2020 14:11:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:11:02: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 10 Aug 2020 14:11:02: #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 14:11:02: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:11:08: 8000000 INFO @ Mon, 10 Aug 2020 14:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.05_summits.bed INFO @ Mon, 10 Aug 2020 14:11:09: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (1245 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:11:13: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:11:19: 10000000 INFO @ Mon, 10 Aug 2020 14:11:25: 11000000 INFO @ Mon, 10 Aug 2020 14:11:28: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:11:28: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:11:28: #1 total tags in treatment: 11365834 INFO @ Mon, 10 Aug 2020 14:11:28: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:11:28: #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 14:11:28: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:11:28: #1 tags after filtering in treatment: 11365661 INFO @ Mon, 10 Aug 2020 14:11:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:11:28: #1 finished! INFO @ Mon, 10 Aug 2020 14:11:28: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:11:29: #2 number of paired peaks: 6205 INFO @ Mon, 10 Aug 2020 14:11:29: start model_add_line... INFO @ Mon, 10 Aug 2020 14:11:29: start X-correlation... INFO @ Mon, 10 Aug 2020 14:11:29: end of X-cor INFO @ Mon, 10 Aug 2020 14:11:29: #2 finished! INFO @ Mon, 10 Aug 2020 14:11:29: #2 predicted fragment length is 51 bps INFO @ Mon, 10 Aug 2020 14:11:29: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 10 Aug 2020 14:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.20_model.r WARNING @ Mon, 10 Aug 2020 14:11:29: #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 14:11:29: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 10 Aug 2020 14:11:29: #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 14:11:29: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:11:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.10_summits.bed INFO @ Mon, 10 Aug 2020 14:11:40: Done! pass1 - making usageList (31 chroms): 0 millis pass2 - checking and writing primary data (665 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:11:55: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047620/SRX8047620.20_summits.bed INFO @ Mon, 10 Aug 2020 14:12:07: Done! pass1 - making usageList (26 chroms): 0 millis pass2 - checking and writing primary data (304 records, 4 fields): 5 millis CompletedMACS2peakCalling