Job ID = 6627472 SRX = SRX8521321 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:01 Multiseed full-index search: 00:07:00 51597118 reads; of these: 51597118 (100.00%) were unpaired; of these: 41920185 (81.25%) aligned 0 times 7642701 (14.81%) aligned exactly 1 time 2034232 (3.94%) aligned >1 times 18.75% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:01 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] 1833312 / 9676933 = 0.1895 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 @ Tue, 14 Jul 2020 11:53:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.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 @ Tue, 14 Jul 2020 11:53:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:53:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:53:38: 1000000 INFO @ Tue, 14 Jul 2020 11:53:44: 2000000 INFO @ Tue, 14 Jul 2020 11:53:50: 3000000 INFO @ Tue, 14 Jul 2020 11:53:56: 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 @ Tue, 14 Jul 2020 11:54:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.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 @ Tue, 14 Jul 2020 11:54:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:54:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:54:02: 5000000 INFO @ Tue, 14 Jul 2020 11:54:07: 1000000 INFO @ Tue, 14 Jul 2020 11:54:09: 6000000 INFO @ Tue, 14 Jul 2020 11:54:14: 2000000 INFO @ Tue, 14 Jul 2020 11:54:16: 7000000 INFO @ Tue, 14 Jul 2020 11:54:21: 3000000 INFO @ Tue, 14 Jul 2020 11:54:22: #1 tag size is determined as 57 bps INFO @ Tue, 14 Jul 2020 11:54:22: #1 tag size = 57 INFO @ Tue, 14 Jul 2020 11:54:22: #1 total tags in treatment: 7843621 INFO @ Tue, 14 Jul 2020 11:54:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:54:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:54:23: #1 tags after filtering in treatment: 7843432 INFO @ Tue, 14 Jul 2020 11:54:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:54:23: #1 finished! INFO @ Tue, 14 Jul 2020 11:54:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:54:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:54:23: #2 number of paired peaks: 454 WARNING @ Tue, 14 Jul 2020 11:54:23: Fewer paired peaks (454) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 454 pairs to build model! INFO @ Tue, 14 Jul 2020 11:54:23: start model_add_line... INFO @ Tue, 14 Jul 2020 11:54:23: start X-correlation... INFO @ Tue, 14 Jul 2020 11:54:23: end of X-cor INFO @ Tue, 14 Jul 2020 11:54:23: #2 finished! INFO @ Tue, 14 Jul 2020 11:54:23: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 11:54:23: #2 alternative fragment length(s) may be 4,51,550 bps INFO @ Tue, 14 Jul 2020 11:54:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.05_model.r WARNING @ Tue, 14 Jul 2020 11:54:23: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:54:23: #2 You may need to consider one of the other alternative d(s): 4,51,550 WARNING @ Tue, 14 Jul 2020 11:54:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:54:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:54:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:54:27: 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 @ Tue, 14 Jul 2020 11:54:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.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 @ Tue, 14 Jul 2020 11:54:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:54:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:54:34: 5000000 INFO @ Tue, 14 Jul 2020 11:54:38: 1000000 INFO @ Tue, 14 Jul 2020 11:54:39: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:54:42: 6000000 INFO @ Tue, 14 Jul 2020 11:54:46: 2000000 INFO @ Tue, 14 Jul 2020 11:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.05_summits.bed INFO @ Tue, 14 Jul 2020 11:54:47: Done! pass1 - making usageList (213 chroms): 1 millis pass2 - checking and writing primary data (1168 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:54:49: 7000000 INFO @ Tue, 14 Jul 2020 11:54:54: 3000000 INFO @ Tue, 14 Jul 2020 11:54:56: #1 tag size is determined as 57 bps INFO @ Tue, 14 Jul 2020 11:54:56: #1 tag size = 57 INFO @ Tue, 14 Jul 2020 11:54:56: #1 total tags in treatment: 7843621 INFO @ Tue, 14 Jul 2020 11:54:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:54:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:54:56: #1 tags after filtering in treatment: 7843432 INFO @ Tue, 14 Jul 2020 11:54:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:54:56: #1 finished! INFO @ Tue, 14 Jul 2020 11:54:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:54:57: #2 number of paired peaks: 454 WARNING @ Tue, 14 Jul 2020 11:54:57: Fewer paired peaks (454) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 454 pairs to build model! INFO @ Tue, 14 Jul 2020 11:54:57: start model_add_line... INFO @ Tue, 14 Jul 2020 11:54:57: start X-correlation... INFO @ Tue, 14 Jul 2020 11:54:57: end of X-cor INFO @ Tue, 14 Jul 2020 11:54:57: #2 finished! INFO @ Tue, 14 Jul 2020 11:54:57: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 11:54:57: #2 alternative fragment length(s) may be 4,51,550 bps INFO @ Tue, 14 Jul 2020 11:54:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.10_model.r WARNING @ Tue, 14 Jul 2020 11:54:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:54:57: #2 You may need to consider one of the other alternative d(s): 4,51,550 WARNING @ Tue, 14 Jul 2020 11:54:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:54:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:54:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:55:01: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:55:09: 5000000 INFO @ Tue, 14 Jul 2020 11:55:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:55:16: 6000000 INFO @ Tue, 14 Jul 2020 11:55:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:55:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:55:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.10_summits.bed INFO @ Tue, 14 Jul 2020 11:55:21: Done! pass1 - making usageList (140 chroms): 1 millis pass2 - checking and writing primary data (444 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:55:23: 7000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:55:29: #1 tag size is determined as 57 bps INFO @ Tue, 14 Jul 2020 11:55:29: #1 tag size = 57 INFO @ Tue, 14 Jul 2020 11:55:29: #1 total tags in treatment: 7843621 INFO @ Tue, 14 Jul 2020 11:55:29: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:55:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:55:30: #1 tags after filtering in treatment: 7843432 INFO @ Tue, 14 Jul 2020 11:55:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:55:30: #1 finished! INFO @ Tue, 14 Jul 2020 11:55:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:55:30: #2 number of paired peaks: 454 WARNING @ Tue, 14 Jul 2020 11:55:30: Fewer paired peaks (454) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 454 pairs to build model! INFO @ Tue, 14 Jul 2020 11:55:30: start model_add_line... INFO @ Tue, 14 Jul 2020 11:55:30: start X-correlation... INFO @ Tue, 14 Jul 2020 11:55:30: end of X-cor INFO @ Tue, 14 Jul 2020 11:55:30: #2 finished! INFO @ Tue, 14 Jul 2020 11:55:30: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 11:55:30: #2 alternative fragment length(s) may be 4,51,550 bps INFO @ Tue, 14 Jul 2020 11:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.20_model.r WARNING @ Tue, 14 Jul 2020 11:55:31: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:55:31: #2 You may need to consider one of the other alternative d(s): 4,51,550 WARNING @ Tue, 14 Jul 2020 11:55:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:55:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:55:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521321/SRX8521321.20_summits.bed INFO @ Tue, 14 Jul 2020 11:55:55: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 3 millis CompletedMACS2peakCalling