Job ID = 6509087 SRX = SRX645132 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:05:27 prefetch.2.10.7: 1) Downloading 'SRR1505732'... 2020-06-26T15:05:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:11:44 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:11:44 prefetch.2.10.7: 1) 'SRR1505732' was downloaded successfully Read 36000000 spots for SRR1505732/SRR1505732.sra Written 36000000 spots for SRR1505732/SRR1505732.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: 00:12:50 36000000 reads; of these: 36000000 (100.00%) were unpaired; of these: 18720261 (52.00%) aligned 0 times 15075639 (41.88%) aligned exactly 1 time 2204100 (6.12%) aligned >1 times 48.00% overall alignment rate Time searching: 00:12:51 Overall time: 00:12:51 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] 14217524 / 17279739 = 0.8228 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 @ Sat, 27 Jun 2020 00:33:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.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 @ Sat, 27 Jun 2020 00:33:11: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:33:11: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:33:24: 1000000 INFO @ Sat, 27 Jun 2020 00:33:37: 2000000 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 @ Sat, 27 Jun 2020 00:33:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.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 @ Sat, 27 Jun 2020 00:33:41: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:33:41: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:33:52: 3000000 INFO @ Sat, 27 Jun 2020 00:33:52: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:33:52: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:33:52: #1 total tags in treatment: 3062215 INFO @ Sat, 27 Jun 2020 00:33:52: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:33:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:33:53: #1 tags after filtering in treatment: 3062075 INFO @ Sat, 27 Jun 2020 00:33:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:33:53: #1 finished! INFO @ Sat, 27 Jun 2020 00:33:53: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:33:53: 1000000 INFO @ Sat, 27 Jun 2020 00:33:53: #2 number of paired peaks: 7822 INFO @ Sat, 27 Jun 2020 00:33:53: start model_add_line... INFO @ Sat, 27 Jun 2020 00:33:53: start X-correlation... INFO @ Sat, 27 Jun 2020 00:33:54: end of X-cor INFO @ Sat, 27 Jun 2020 00:33:54: #2 finished! INFO @ Sat, 27 Jun 2020 00:33:54: #2 predicted fragment length is 134 bps INFO @ Sat, 27 Jun 2020 00:33:54: #2 alternative fragment length(s) may be 4,134 bps INFO @ Sat, 27 Jun 2020 00:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.05_model.r WARNING @ Sat, 27 Jun 2020 00:33:54: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:33:54: #2 You may need to consider one of the other alternative d(s): 4,134 WARNING @ Sat, 27 Jun 2020 00:33:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:33:54: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:34:01: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:34:05: 2000000 INFO @ Sat, 27 Jun 2020 00:34:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:34:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:34:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.05_summits.bed INFO @ Sat, 27 Jun 2020 00:34:06: Done! pass1 - making usageList (543 chroms): 2 millis pass2 - checking and writing primary data (4213 records, 4 fields): 54 millis CompletedMACS2peakCalling 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 @ Sat, 27 Jun 2020 00:34:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.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 @ Sat, 27 Jun 2020 00:34:11: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:34:11: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:34:18: 3000000 INFO @ Sat, 27 Jun 2020 00:34:19: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:34:19: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:34:19: #1 total tags in treatment: 3062215 INFO @ Sat, 27 Jun 2020 00:34:19: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:34:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:34:19: #1 tags after filtering in treatment: 3062075 INFO @ Sat, 27 Jun 2020 00:34:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:34:19: #1 finished! INFO @ Sat, 27 Jun 2020 00:34:19: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:34:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:34:20: #2 number of paired peaks: 7822 INFO @ Sat, 27 Jun 2020 00:34:20: start model_add_line... INFO @ Sat, 27 Jun 2020 00:34:20: start X-correlation... INFO @ Sat, 27 Jun 2020 00:34:20: end of X-cor INFO @ Sat, 27 Jun 2020 00:34:20: #2 finished! INFO @ Sat, 27 Jun 2020 00:34:20: #2 predicted fragment length is 134 bps INFO @ Sat, 27 Jun 2020 00:34:20: #2 alternative fragment length(s) may be 4,134 bps INFO @ Sat, 27 Jun 2020 00:34:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.10_model.r WARNING @ Sat, 27 Jun 2020 00:34:20: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:34:20: #2 You may need to consider one of the other alternative d(s): 4,134 WARNING @ Sat, 27 Jun 2020 00:34:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:34:20: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:34:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:34:23: 1000000 INFO @ Sat, 27 Jun 2020 00:34:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:34:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:34:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:34:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.10_summits.bed INFO @ Sat, 27 Jun 2020 00:34:32: Done! pass1 - making usageList (417 chroms): 1 millis pass2 - checking and writing primary data (1421 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:34:34: 2000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:34:47: 3000000 INFO @ Sat, 27 Jun 2020 00:34:47: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:34:47: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:34:47: #1 total tags in treatment: 3062215 INFO @ Sat, 27 Jun 2020 00:34:47: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:34:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:34:48: #1 tags after filtering in treatment: 3062075 INFO @ Sat, 27 Jun 2020 00:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:34:48: #1 finished! INFO @ Sat, 27 Jun 2020 00:34:48: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:34:49: #2 number of paired peaks: 7822 INFO @ Sat, 27 Jun 2020 00:34:49: start model_add_line... INFO @ Sat, 27 Jun 2020 00:34:49: start X-correlation... INFO @ Sat, 27 Jun 2020 00:34:49: end of X-cor INFO @ Sat, 27 Jun 2020 00:34:49: #2 finished! INFO @ Sat, 27 Jun 2020 00:34:49: #2 predicted fragment length is 134 bps INFO @ Sat, 27 Jun 2020 00:34:49: #2 alternative fragment length(s) may be 4,134 bps INFO @ Sat, 27 Jun 2020 00:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.20_model.r WARNING @ Sat, 27 Jun 2020 00:34:49: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:34:49: #2 You may need to consider one of the other alternative d(s): 4,134 WARNING @ Sat, 27 Jun 2020 00:34:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:34:49: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:34:57: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:35:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:35:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:35:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645132/SRX645132.20_summits.bed INFO @ Sat, 27 Jun 2020 00:35:01: Done! pass1 - making usageList (255 chroms): 1 millis pass2 - checking and writing primary data (399 records, 4 fields): 19 millis CompletedMACS2peakCalling