Job ID = 6627351 SRX = SRX8521289 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: 00:00:00 Multiseed full-index search: 00:07:13 53151957 reads; of these: 53151957 (100.00%) were unpaired; of these: 45616727 (85.82%) aligned 0 times 5795435 (10.90%) aligned exactly 1 time 1739795 (3.27%) aligned >1 times 14.18% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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] 1380435 / 7535230 = 0.1832 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 11:18:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.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 11:18:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:18:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:18:27: 1000000 INFO @ Tue, 14 Jul 2020 11:18:33: 2000000 INFO @ Tue, 14 Jul 2020 11:18:38: 3000000 INFO @ Tue, 14 Jul 2020 11:18:45: 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 11:18:50: 5000000 INFO @ Tue, 14 Jul 2020 11:18:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.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 11:18:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:18:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:18:56: 6000000 INFO @ Tue, 14 Jul 2020 11:18:58: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:18:58: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:18:58: #1 total tags in treatment: 6154795 INFO @ Tue, 14 Jul 2020 11:18:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:18:58: #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 11:18:58: #1 tags after filtering in treatment: 6154605 INFO @ Tue, 14 Jul 2020 11:18:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:18:58: #1 finished! INFO @ Tue, 14 Jul 2020 11:18:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:18:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:18:59: #2 number of paired peaks: 678 WARNING @ Tue, 14 Jul 2020 11:18:59: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Tue, 14 Jul 2020 11:18:59: start model_add_line... INFO @ Tue, 14 Jul 2020 11:18:59: start X-correlation... INFO @ Tue, 14 Jul 2020 11:18:59: end of X-cor INFO @ Tue, 14 Jul 2020 11:18:59: #2 finished! INFO @ Tue, 14 Jul 2020 11:18:59: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:18:59: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:18:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.05_model.r WARNING @ Tue, 14 Jul 2020 11:18:59: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:18:59: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:18:59: #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 11:18:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:19:00: 1000000 INFO @ Tue, 14 Jul 2020 11:19:08: 2000000 INFO @ Tue, 14 Jul 2020 11:19:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:19:14: 3000000 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 11:19:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:19:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:19:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.05_summits.bed INFO @ Tue, 14 Jul 2020 11:19:20: Done! pass1 - making usageList (219 chroms): 1 millis pass2 - checking and writing primary data (1752 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.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 11:19:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:19:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:19:21: 4000000 INFO @ Tue, 14 Jul 2020 11:19:27: 1000000 INFO @ Tue, 14 Jul 2020 11:19:30: 5000000 INFO @ Tue, 14 Jul 2020 11:19:33: 2000000 INFO @ Tue, 14 Jul 2020 11:19:38: 6000000 INFO @ Tue, 14 Jul 2020 11:19:38: 3000000 INFO @ Tue, 14 Jul 2020 11:19:39: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:19:39: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:19:39: #1 total tags in treatment: 6154795 INFO @ Tue, 14 Jul 2020 11:19:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:19:39: #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 11:19:39: #1 tags after filtering in treatment: 6154605 INFO @ Tue, 14 Jul 2020 11:19:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:19:39: #1 finished! INFO @ Tue, 14 Jul 2020 11:19:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:19:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:19:40: #2 number of paired peaks: 678 WARNING @ Tue, 14 Jul 2020 11:19:40: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Tue, 14 Jul 2020 11:19:40: start model_add_line... INFO @ Tue, 14 Jul 2020 11:19:40: start X-correlation... INFO @ Tue, 14 Jul 2020 11:19:40: end of X-cor INFO @ Tue, 14 Jul 2020 11:19:40: #2 finished! INFO @ Tue, 14 Jul 2020 11:19:40: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:19:40: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:19:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.10_model.r WARNING @ Tue, 14 Jul 2020 11:19:40: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:19:40: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:19:40: #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 11:19:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:19:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:19:44: 4000000 INFO @ Tue, 14 Jul 2020 11:19:50: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:19:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:19:56: 6000000 INFO @ Tue, 14 Jul 2020 11:19:57: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:19:57: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:19:57: #1 total tags in treatment: 6154795 INFO @ Tue, 14 Jul 2020 11:19:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:19:57: #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 11:19:57: #1 tags after filtering in treatment: 6154605 INFO @ Tue, 14 Jul 2020 11:19:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:19:57: #1 finished! INFO @ Tue, 14 Jul 2020 11:19:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:19:58: #2 number of paired peaks: 678 WARNING @ Tue, 14 Jul 2020 11:19:58: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Tue, 14 Jul 2020 11:19:58: start model_add_line... INFO @ Tue, 14 Jul 2020 11:19:58: start X-correlation... INFO @ Tue, 14 Jul 2020 11:19:58: end of X-cor INFO @ Tue, 14 Jul 2020 11:19:58: #2 finished! INFO @ Tue, 14 Jul 2020 11:19:58: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:19:58: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.20_model.r WARNING @ Tue, 14 Jul 2020 11:19:58: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:19:58: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:19:58: #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 11:19:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:19:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:20:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:20:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.10_summits.bed INFO @ Tue, 14 Jul 2020 11:20:01: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:20:11: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:20:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:20:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:20:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521289/SRX8521289.20_summits.bed INFO @ Tue, 14 Jul 2020 11:20:17: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 3 millis CompletedMACS2peakCalling