Job ID = 8184364 SRX = SRX8047588 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:17:16 prefetch.2.10.7: 1) Downloading 'SRR11471313'... 2020-08-10T03:17:16 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:18:00 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:18:01 prefetch.2.10.7: 'SRR11471313' is valid 2020-08-10T03:18:01 prefetch.2.10.7: 1) 'SRR11471313' was downloaded successfully Read 12559729 spots for SRR11471313/SRR11471313.sra Written 12559729 spots for SRR11471313/SRR11471313.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: 00:37:51 12559729 reads; of these: 12559729 (100.00%) were unpaired; of these: 1334223 (10.62%) aligned 0 times 5050208 (40.21%) aligned exactly 1 time 6175298 (49.17%) aligned >1 times 89.38% overall alignment rate Time searching: 00:37:54 Overall time: 00:37:54 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] 974554 / 11225506 = 0.0868 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 13:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.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 13:00:03: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:00:03: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:00:08: 1000000 INFO @ Mon, 10 Aug 2020 13:00:13: 2000000 INFO @ Mon, 10 Aug 2020 13:00:18: 3000000 INFO @ Mon, 10 Aug 2020 13:00:22: 4000000 INFO @ Mon, 10 Aug 2020 13:00:27: 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 13:00:32: 6000000 INFO @ Mon, 10 Aug 2020 13:00:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.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 13:00:33: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:00:33: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:00:37: 7000000 INFO @ Mon, 10 Aug 2020 13:00:38: 1000000 INFO @ Mon, 10 Aug 2020 13:00:42: 8000000 INFO @ Mon, 10 Aug 2020 13:00:43: 2000000 INFO @ Mon, 10 Aug 2020 13:00:46: 9000000 INFO @ Mon, 10 Aug 2020 13:00:48: 3000000 INFO @ Mon, 10 Aug 2020 13:00:51: 10000000 INFO @ Mon, 10 Aug 2020 13:00:53: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:00:53: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:00:53: #1 total tags in treatment: 10250952 INFO @ Mon, 10 Aug 2020 13:00:53: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:00:53: #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 13:00:53: 4000000 INFO @ Mon, 10 Aug 2020 13:00:53: #1 tags after filtering in treatment: 10250794 INFO @ Mon, 10 Aug 2020 13:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:00:53: #1 finished! INFO @ Mon, 10 Aug 2020 13:00:53: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:00:55: #2 number of paired peaks: 43791 INFO @ Mon, 10 Aug 2020 13:00:55: start model_add_line... INFO @ Mon, 10 Aug 2020 13:00:55: start X-correlation... INFO @ Mon, 10 Aug 2020 13:00:55: end of X-cor INFO @ Mon, 10 Aug 2020 13:00:55: #2 finished! INFO @ Mon, 10 Aug 2020 13:00:55: #2 predicted fragment length is 59 bps INFO @ Mon, 10 Aug 2020 13:00:55: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 10 Aug 2020 13:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.05_model.r WARNING @ Mon, 10 Aug 2020 13:00:55: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:00:55: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 10 Aug 2020 13:00:55: #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 13:00:55: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:00:58: 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 13:01:02: 6000000 INFO @ Mon, 10 Aug 2020 13:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.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 13:01:03: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:01:03: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:01:07: 7000000 INFO @ Mon, 10 Aug 2020 13:01:08: 1000000 INFO @ Mon, 10 Aug 2020 13:01:12: 8000000 INFO @ Mon, 10 Aug 2020 13:01:13: 2000000 INFO @ Mon, 10 Aug 2020 13:01:17: 9000000 INFO @ Mon, 10 Aug 2020 13:01:18: 3000000 INFO @ Mon, 10 Aug 2020 13:01:19: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:01:22: 10000000 INFO @ Mon, 10 Aug 2020 13:01:23: 4000000 INFO @ Mon, 10 Aug 2020 13:01:23: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:01:23: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:01:23: #1 total tags in treatment: 10250952 INFO @ Mon, 10 Aug 2020 13:01:23: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:01:23: #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 13:01:24: #1 tags after filtering in treatment: 10250794 INFO @ Mon, 10 Aug 2020 13:01:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:01:24: #1 finished! INFO @ Mon, 10 Aug 2020 13:01:24: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:01:26: #2 number of paired peaks: 43791 INFO @ Mon, 10 Aug 2020 13:01:26: start model_add_line... INFO @ Mon, 10 Aug 2020 13:01:26: start X-correlation... INFO @ Mon, 10 Aug 2020 13:01:26: end of X-cor INFO @ Mon, 10 Aug 2020 13:01:26: #2 finished! INFO @ Mon, 10 Aug 2020 13:01:26: #2 predicted fragment length is 59 bps INFO @ Mon, 10 Aug 2020 13:01:26: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 10 Aug 2020 13:01:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.10_model.r WARNING @ Mon, 10 Aug 2020 13:01:26: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:01:26: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 10 Aug 2020 13:01:26: #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 13:01:26: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:01:28: 5000000 INFO @ Mon, 10 Aug 2020 13:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.05_summits.bed INFO @ Mon, 10 Aug 2020 13:01:30: Done! pass1 - making usageList (84 chroms): 2 millis pass2 - checking and writing primary data (11879 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:01:32: 6000000 INFO @ Mon, 10 Aug 2020 13:01:37: 7000000 INFO @ Mon, 10 Aug 2020 13:01:42: 8000000 INFO @ Mon, 10 Aug 2020 13:01:47: 9000000 INFO @ Mon, 10 Aug 2020 13:01:48: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:01:51: 10000000 INFO @ Mon, 10 Aug 2020 13:01:53: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:01:53: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:01:53: #1 total tags in treatment: 10250952 INFO @ Mon, 10 Aug 2020 13:01:53: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:01:53: #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 13:01:53: #1 tags after filtering in treatment: 10250794 INFO @ Mon, 10 Aug 2020 13:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:01:53: #1 finished! INFO @ Mon, 10 Aug 2020 13:01:53: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:01:55: #2 number of paired peaks: 43791 INFO @ Mon, 10 Aug 2020 13:01:55: start model_add_line... INFO @ Mon, 10 Aug 2020 13:01:55: start X-correlation... INFO @ Mon, 10 Aug 2020 13:01:55: end of X-cor INFO @ Mon, 10 Aug 2020 13:01:55: #2 finished! INFO @ Mon, 10 Aug 2020 13:01:55: #2 predicted fragment length is 59 bps INFO @ Mon, 10 Aug 2020 13:01:55: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 10 Aug 2020 13:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.20_model.r WARNING @ Mon, 10 Aug 2020 13:01:55: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:01:55: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 10 Aug 2020 13:01:55: #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 13:01:55: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:01:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.10_summits.bed INFO @ Mon, 10 Aug 2020 13:01:59: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (2718 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:02:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047588/SRX8047588.20_summits.bed INFO @ Mon, 10 Aug 2020 13:02:29: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (699 records, 4 fields): 3 millis CompletedMACS2peakCalling