Job ID = 14171806 SRX = SRX9986152 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: 00:03:34 14983892 reads; of these: 14983892 (100.00%) were unpaired; of these: 2701052 (18.03%) aligned 0 times 9295068 (62.03%) aligned exactly 1 time 2987772 (19.94%) aligned >1 times 81.97% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 2087331 / 12282840 = 0.1699 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:02:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.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, 11 Dec 2021 13:02:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:02:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:02:51: 1000000 INFO @ Sat, 11 Dec 2021 13:02:57: 2000000 INFO @ Sat, 11 Dec 2021 13:03:03: 3000000 INFO @ Sat, 11 Dec 2021 13:03:08: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:03:14: 5000000 INFO @ Sat, 11 Dec 2021 13:03:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.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, 11 Dec 2021 13:03:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:03:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:03:20: 6000000 INFO @ Sat, 11 Dec 2021 13:03:23: 1000000 INFO @ Sat, 11 Dec 2021 13:03:28: 7000000 INFO @ Sat, 11 Dec 2021 13:03:30: 2000000 INFO @ Sat, 11 Dec 2021 13:03:34: 8000000 INFO @ Sat, 11 Dec 2021 13:03:37: 3000000 INFO @ Sat, 11 Dec 2021 13:03:41: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:03:44: 4000000 INFO @ Sat, 11 Dec 2021 13:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.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, 11 Dec 2021 13:03:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:03:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:03:48: 10000000 INFO @ Sat, 11 Dec 2021 13:03:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:03:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:03:50: #1 total tags in treatment: 10195509 INFO @ Sat, 11 Dec 2021 13:03:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:03:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:03:50: #1 tags after filtering in treatment: 10195408 INFO @ Sat, 11 Dec 2021 13:03:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:03:50: #1 finished! INFO @ Sat, 11 Dec 2021 13:03:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:03:51: 5000000 INFO @ Sat, 11 Dec 2021 13:03:51: #2 number of paired peaks: 286 WARNING @ Sat, 11 Dec 2021 13:03:51: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Sat, 11 Dec 2021 13:03:51: start model_add_line... INFO @ Sat, 11 Dec 2021 13:03:51: start X-correlation... INFO @ Sat, 11 Dec 2021 13:03:51: end of X-cor INFO @ Sat, 11 Dec 2021 13:03:51: #2 finished! INFO @ Sat, 11 Dec 2021 13:03:51: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 13:03:51: #2 alternative fragment length(s) may be 43,58,85,107,491,541 bps INFO @ Sat, 11 Dec 2021 13:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.05_model.r WARNING @ Sat, 11 Dec 2021 13:03:51: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:03:51: #2 You may need to consider one of the other alternative d(s): 43,58,85,107,491,541 WARNING @ Sat, 11 Dec 2021 13:03:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:03:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:03:53: 1000000 INFO @ Sat, 11 Dec 2021 13:03:58: 6000000 INFO @ Sat, 11 Dec 2021 13:04:01: 2000000 INFO @ Sat, 11 Dec 2021 13:04:05: 7000000 INFO @ Sat, 11 Dec 2021 13:04:09: 3000000 INFO @ Sat, 11 Dec 2021 13:04:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:04:13: 8000000 INFO @ Sat, 11 Dec 2021 13:04:17: 4000000 INFO @ Sat, 11 Dec 2021 13:04:20: 9000000 INFO @ Sat, 11 Dec 2021 13:04:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:04:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:04:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.05_summits.bed INFO @ Sat, 11 Dec 2021 13:04:21: Done! pass1 - making usageList (237 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:04:25: 5000000 INFO @ Sat, 11 Dec 2021 13:04:28: 10000000 INFO @ Sat, 11 Dec 2021 13:04:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:04:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:04:29: #1 total tags in treatment: 10195509 INFO @ Sat, 11 Dec 2021 13:04:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:04:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:04:29: #1 tags after filtering in treatment: 10195408 INFO @ Sat, 11 Dec 2021 13:04:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:04:29: #1 finished! INFO @ Sat, 11 Dec 2021 13:04:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:04:29: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:04:30: #2 number of paired peaks: 286 WARNING @ Sat, 11 Dec 2021 13:04:30: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Sat, 11 Dec 2021 13:04:30: start model_add_line... INFO @ Sat, 11 Dec 2021 13:04:30: start X-correlation... INFO @ Sat, 11 Dec 2021 13:04:30: end of X-cor INFO @ Sat, 11 Dec 2021 13:04:30: #2 finished! INFO @ Sat, 11 Dec 2021 13:04:30: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 13:04:30: #2 alternative fragment length(s) may be 43,58,85,107,491,541 bps INFO @ Sat, 11 Dec 2021 13:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.10_model.r WARNING @ Sat, 11 Dec 2021 13:04:30: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:04:30: #2 You may need to consider one of the other alternative d(s): 43,58,85,107,491,541 WARNING @ Sat, 11 Dec 2021 13:04:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:04:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:04:32: 6000000 INFO @ Sat, 11 Dec 2021 13:04:39: 7000000 INFO @ Sat, 11 Dec 2021 13:04:46: 8000000 INFO @ Sat, 11 Dec 2021 13:04:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:04:54: 9000000 INFO @ Sat, 11 Dec 2021 13:05:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:05:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:05:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.10_summits.bed INFO @ Sat, 11 Dec 2021 13:05:00: Done! pass1 - making usageList (84 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:05:01: 10000000 INFO @ Sat, 11 Dec 2021 13:05:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:05:02: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:05:02: #1 total tags in treatment: 10195509 INFO @ Sat, 11 Dec 2021 13:05:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:05:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:05:03: #1 tags after filtering in treatment: 10195408 INFO @ Sat, 11 Dec 2021 13:05:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:05:03: #1 finished! INFO @ Sat, 11 Dec 2021 13:05:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:05:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:05:03: #2 number of paired peaks: 286 WARNING @ Sat, 11 Dec 2021 13:05:03: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Sat, 11 Dec 2021 13:05:03: start model_add_line... INFO @ Sat, 11 Dec 2021 13:05:03: start X-correlation... INFO @ Sat, 11 Dec 2021 13:05:03: end of X-cor INFO @ Sat, 11 Dec 2021 13:05:03: #2 finished! INFO @ Sat, 11 Dec 2021 13:05:03: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 13:05:03: #2 alternative fragment length(s) may be 43,58,85,107,491,541 bps INFO @ Sat, 11 Dec 2021 13:05:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.20_model.r WARNING @ Sat, 11 Dec 2021 13:05:03: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:05:03: #2 You may need to consider one of the other alternative d(s): 43,58,85,107,491,541 WARNING @ Sat, 11 Dec 2021 13:05:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:05:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:05:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:05:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986152/SRX9986152.20_summits.bed INFO @ Sat, 11 Dec 2021 13:05:33: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling