Job ID = 6454230 SRX = SRX193309 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:17:09 prefetch.2.10.7: 1) Downloading 'SRR585042'... 2020-06-21T09:17:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:21:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:21:10 prefetch.2.10.7: 'SRR585042' is valid 2020-06-21T09:21:10 prefetch.2.10.7: 1) 'SRR585042' was downloaded successfully Read 13175817 spots for SRR585042/SRR585042.sra Written 13175817 spots for SRR585042/SRR585042.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:07 13175817 reads; of these: 13175817 (100.00%) were unpaired; of these: 895868 (6.80%) aligned 0 times 8371343 (63.54%) aligned exactly 1 time 3908606 (29.66%) aligned >1 times 93.20% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1352912 / 12279949 = 0.1102 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 @ Sun, 21 Jun 2020 18:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:29:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:29:32: 1000000 INFO @ Sun, 21 Jun 2020 18:29:37: 2000000 INFO @ Sun, 21 Jun 2020 18:29:43: 3000000 INFO @ Sun, 21 Jun 2020 18:29:48: 4000000 INFO @ Sun, 21 Jun 2020 18:29:54: 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 @ Sun, 21 Jun 2020 18:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:29:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:00: 6000000 INFO @ Sun, 21 Jun 2020 18:30:03: 1000000 INFO @ Sun, 21 Jun 2020 18:30:06: 7000000 INFO @ Sun, 21 Jun 2020 18:30:09: 2000000 INFO @ Sun, 21 Jun 2020 18:30:12: 8000000 INFO @ Sun, 21 Jun 2020 18:30:15: 3000000 INFO @ Sun, 21 Jun 2020 18:30:18: 9000000 INFO @ Sun, 21 Jun 2020 18:30:21: 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 @ Sun, 21 Jun 2020 18:30:25: 10000000 INFO @ Sun, 21 Jun 2020 18:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:30:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:27: 5000000 INFO @ Sun, 21 Jun 2020 18:30:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:30:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:30:31: #1 total tags in treatment: 10927037 INFO @ Sun, 21 Jun 2020 18:30:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:30:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:30:31: #1 tags after filtering in treatment: 10926953 INFO @ Sun, 21 Jun 2020 18:30:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:30:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:30:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:30:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:30:32: #2 number of paired peaks: 1613 INFO @ Sun, 21 Jun 2020 18:30:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:30:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:30:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:30:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:30:32: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:30:32: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 21 Jun 2020 18:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.05_model.r WARNING @ Sun, 21 Jun 2020 18:30:32: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:30:32: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 21 Jun 2020 18:30:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:30:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:30:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:30:32: 1000000 INFO @ Sun, 21 Jun 2020 18:30:33: 6000000 INFO @ Sun, 21 Jun 2020 18:30:39: 2000000 INFO @ Sun, 21 Jun 2020 18:30:39: 7000000 INFO @ Sun, 21 Jun 2020 18:30:45: 3000000 INFO @ Sun, 21 Jun 2020 18:30:45: 8000000 INFO @ Sun, 21 Jun 2020 18:30:51: 4000000 INFO @ Sun, 21 Jun 2020 18:30:51: 9000000 INFO @ Sun, 21 Jun 2020 18:30:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:30:57: 5000000 INFO @ Sun, 21 Jun 2020 18:30:58: 10000000 INFO @ Sun, 21 Jun 2020 18:31:03: 6000000 INFO @ Sun, 21 Jun 2020 18:31:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:31:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:31:04: #1 total tags in treatment: 10927037 INFO @ Sun, 21 Jun 2020 18:31:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:31:04: #1 tags after filtering in treatment: 10926953 INFO @ Sun, 21 Jun 2020 18:31:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:05: #2 number of paired peaks: 1613 INFO @ Sun, 21 Jun 2020 18:31:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:05: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:31:05: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 21 Jun 2020 18:31:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.10_model.r INFO @ Sun, 21 Jun 2020 18:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.05_summits.bed WARNING @ Sun, 21 Jun 2020 18:31:05: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:31:05: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 21 Jun 2020 18:31:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:31:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:31:05: Done! pass1 - making usageList (569 chroms): 1 millis pass2 - checking and writing primary data (2530 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:31:09: 7000000 INFO @ Sun, 21 Jun 2020 18:31:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:31:20: 9000000 INFO @ Sun, 21 Jun 2020 18:31:26: 10000000 INFO @ Sun, 21 Jun 2020 18:31:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:31:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:31:31: #1 total tags in treatment: 10927037 INFO @ Sun, 21 Jun 2020 18:31:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:31:32: #1 tags after filtering in treatment: 10926953 INFO @ Sun, 21 Jun 2020 18:31:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:33: #2 number of paired peaks: 1613 INFO @ Sun, 21 Jun 2020 18:31:33: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:33: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:31:33: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 21 Jun 2020 18:31:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.20_model.r WARNING @ Sun, 21 Jun 2020 18:31:33: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:31:33: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 21 Jun 2020 18:31:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:31:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.10_summits.bed INFO @ Sun, 21 Jun 2020 18:31:38: Done! pass1 - making usageList (492 chroms): 1 millis pass2 - checking and writing primary data (1875 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:31:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:32:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193309/SRX193309.20_summits.bed INFO @ Sun, 21 Jun 2020 18:32:05: Done! pass1 - making usageList (361 chroms): 1 millis pass2 - checking and writing primary data (844 records, 4 fields): 11 millis CompletedMACS2peakCalling