Job ID = 6459745 SRX = SRX7672886 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:31:01 prefetch.2.10.7: 1) Downloading 'SRR11017733'... 2020-06-21T13:31:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:33:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:33:58 prefetch.2.10.7: 1) 'SRR11017733' was downloaded successfully Read 19646289 spots for SRR11017733/SRR11017733.sra Written 19646289 spots for SRR11017733/SRR11017733.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: 00:02:23 19646289 reads; of these: 19646289 (100.00%) were unpaired; of these: 16269924 (82.81%) aligned 0 times 2486518 (12.66%) aligned exactly 1 time 889847 (4.53%) aligned >1 times 17.19% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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_rmdupse_core] 393869 / 3376365 = 0.1167 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 22:38:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.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 22:38:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:38:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:38:57: 1000000 INFO @ Sun, 21 Jun 2020 22:39:03: 2000000 INFO @ Sun, 21 Jun 2020 22:39:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:39:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:39:10: #1 total tags in treatment: 2982496 INFO @ Sun, 21 Jun 2020 22:39:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:39:10: #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 22:39:10: #1 tags after filtering in treatment: 2982437 INFO @ Sun, 21 Jun 2020 22:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:39:10: #1 finished! INFO @ Sun, 21 Jun 2020 22:39:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:39:10: #2 number of paired peaks: 540 WARNING @ Sun, 21 Jun 2020 22:39:10: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Sun, 21 Jun 2020 22:39:10: start model_add_line... INFO @ Sun, 21 Jun 2020 22:39:10: start X-correlation... INFO @ Sun, 21 Jun 2020 22:39:10: end of X-cor INFO @ Sun, 21 Jun 2020 22:39:10: #2 finished! INFO @ Sun, 21 Jun 2020 22:39:10: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 22:39:10: #2 alternative fragment length(s) may be 56,547 bps INFO @ Sun, 21 Jun 2020 22:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.05_model.r WARNING @ Sun, 21 Jun 2020 22:39:10: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:39:10: #2 You may need to consider one of the other alternative d(s): 56,547 WARNING @ Sun, 21 Jun 2020 22:39:10: #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 22:39:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:39:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:39:18: #3 Call peaks for each chromosome... 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 22:39:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.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 22:39:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:39:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:39:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.05_summits.bed INFO @ Sun, 21 Jun 2020 22:39:21: Done! pass1 - making usageList (353 chroms): 1 millis pass2 - checking and writing primary data (740 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:39:27: 1000000 INFO @ Sun, 21 Jun 2020 22:39:33: 2000000 INFO @ Sun, 21 Jun 2020 22:39:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:39:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:39:39: #1 total tags in treatment: 2982496 INFO @ Sun, 21 Jun 2020 22:39:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:39:39: #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 22:39:39: #1 tags after filtering in treatment: 2982437 INFO @ Sun, 21 Jun 2020 22:39:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:39:39: #1 finished! INFO @ Sun, 21 Jun 2020 22:39:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:39:40: #2 number of paired peaks: 540 WARNING @ Sun, 21 Jun 2020 22:39:40: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Sun, 21 Jun 2020 22:39:40: start model_add_line... INFO @ Sun, 21 Jun 2020 22:39:40: start X-correlation... INFO @ Sun, 21 Jun 2020 22:39:40: end of X-cor INFO @ Sun, 21 Jun 2020 22:39:40: #2 finished! INFO @ Sun, 21 Jun 2020 22:39:40: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 22:39:40: #2 alternative fragment length(s) may be 56,547 bps INFO @ Sun, 21 Jun 2020 22:39:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.10_model.r WARNING @ Sun, 21 Jun 2020 22:39:40: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:39:40: #2 You may need to consider one of the other alternative d(s): 56,547 WARNING @ Sun, 21 Jun 2020 22:39:40: #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 22:39:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:39:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:39:47: #3 Call peaks for each chromosome... 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 22:39:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.10_summits.bed INFO @ Sun, 21 Jun 2020 22:39:50: Done! INFO @ Sun, 21 Jun 2020 22:39:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.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 22:39:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:39:50: #1 read treatment tags... pass1 - making usageList (167 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:39:56: 1000000 INFO @ Sun, 21 Jun 2020 22:40:02: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:40:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:40:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:40:09: #1 total tags in treatment: 2982496 INFO @ Sun, 21 Jun 2020 22:40:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:40:09: #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 22:40:09: #1 tags after filtering in treatment: 2982437 INFO @ Sun, 21 Jun 2020 22:40:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:40:09: #1 finished! INFO @ Sun, 21 Jun 2020 22:40:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:40:10: #2 number of paired peaks: 540 WARNING @ Sun, 21 Jun 2020 22:40:10: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Sun, 21 Jun 2020 22:40:10: start model_add_line... INFO @ Sun, 21 Jun 2020 22:40:10: start X-correlation... INFO @ Sun, 21 Jun 2020 22:40:10: end of X-cor INFO @ Sun, 21 Jun 2020 22:40:10: #2 finished! INFO @ Sun, 21 Jun 2020 22:40:10: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 22:40:10: #2 alternative fragment length(s) may be 56,547 bps INFO @ Sun, 21 Jun 2020 22:40:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.20_model.r WARNING @ Sun, 21 Jun 2020 22:40:10: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:40:10: #2 You may need to consider one of the other alternative d(s): 56,547 WARNING @ Sun, 21 Jun 2020 22:40:10: #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 22:40:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:40:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:40:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:40:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:40:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:40:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672886/SRX7672886.20_summits.bed INFO @ Sun, 21 Jun 2020 22:40:20: Done! pass1 - making usageList (111 chroms): 0 millis pass2 - checking and writing primary data (205 records, 4 fields): 5 millis CompletedMACS2peakCalling