Job ID = 16439137 SRX = SRX15206526 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: 00:10:29 12722405 reads; of these: 12722405 (100.00%) were unpaired; of these: 867137 (6.82%) aligned 0 times 10068005 (79.14%) aligned exactly 1 time 1787263 (14.05%) aligned >1 times 93.18% overall alignment rate Time searching: 00:10:29 Overall time: 00:10:29 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 12 files... [bam_rmdupse_core] 3361117 / 11855268 = 0.2835 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.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, 02 Aug 2022 14:54:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:54:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:55:01: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:55:15: 2000000 INFO @ Tue, 02 Aug 2022 14:55:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.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, 02 Aug 2022 14:55:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:55:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:55:29: 3000000 INFO @ Tue, 02 Aug 2022 14:55:29: 1000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:55:43: 4000000 INFO @ Tue, 02 Aug 2022 14:55:43: 2000000 INFO @ Tue, 02 Aug 2022 14:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.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, 02 Aug 2022 14:55:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:55:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:55:57: 5000000 INFO @ Tue, 02 Aug 2022 14:55:58: 3000000 INFO @ Tue, 02 Aug 2022 14:56:01: 1000000 INFO @ Tue, 02 Aug 2022 14:56:12: 6000000 INFO @ Tue, 02 Aug 2022 14:56:13: 4000000 INFO @ Tue, 02 Aug 2022 14:56:16: 2000000 INFO @ Tue, 02 Aug 2022 14:56:28: 7000000 INFO @ Tue, 02 Aug 2022 14:56:29: 5000000 INFO @ Tue, 02 Aug 2022 14:56:32: 3000000 INFO @ Tue, 02 Aug 2022 14:56:44: 6000000 INFO @ Tue, 02 Aug 2022 14:56:44: 8000000 INFO @ Tue, 02 Aug 2022 14:56:47: 4000000 INFO @ Tue, 02 Aug 2022 14:56:52: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:56:52: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:56:52: #1 total tags in treatment: 8494151 INFO @ Tue, 02 Aug 2022 14:56:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:56:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:56:52: #1 tags after filtering in treatment: 8493953 INFO @ Tue, 02 Aug 2022 14:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:56:52: #1 finished! INFO @ Tue, 02 Aug 2022 14:56:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:56:53: #2 number of paired peaks: 412 WARNING @ Tue, 02 Aug 2022 14:56:53: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 02 Aug 2022 14:56:53: start model_add_line... INFO @ Tue, 02 Aug 2022 14:56:53: start X-correlation... INFO @ Tue, 02 Aug 2022 14:56:53: end of X-cor INFO @ Tue, 02 Aug 2022 14:56:53: #2 finished! INFO @ Tue, 02 Aug 2022 14:56:53: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 14:56:53: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 14:56:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.05_model.r WARNING @ Tue, 02 Aug 2022 14:56:53: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:56:53: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 14:56:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:56:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:56:59: 7000000 INFO @ Tue, 02 Aug 2022 14:57:02: 5000000 INFO @ Tue, 02 Aug 2022 14:57:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:57:14: 8000000 INFO @ Tue, 02 Aug 2022 14:57:17: 6000000 INFO @ Tue, 02 Aug 2022 14:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.05_summits.bed INFO @ Tue, 02 Aug 2022 14:57:20: Done! pass1 - making usageList (356 chroms): 2 millis pass2 - checking and writing primary data (812 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:57:22: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:57:22: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:57:22: #1 total tags in treatment: 8494151 INFO @ Tue, 02 Aug 2022 14:57:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:57:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:57:23: #1 tags after filtering in treatment: 8493953 INFO @ Tue, 02 Aug 2022 14:57:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:57:23: #1 finished! INFO @ Tue, 02 Aug 2022 14:57:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:57:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:57:23: #2 number of paired peaks: 412 WARNING @ Tue, 02 Aug 2022 14:57:23: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 02 Aug 2022 14:57:23: start model_add_line... INFO @ Tue, 02 Aug 2022 14:57:23: start X-correlation... INFO @ Tue, 02 Aug 2022 14:57:23: end of X-cor INFO @ Tue, 02 Aug 2022 14:57:23: #2 finished! INFO @ Tue, 02 Aug 2022 14:57:23: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 14:57:23: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 14:57:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.10_model.r WARNING @ Tue, 02 Aug 2022 14:57:23: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:57:23: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 14:57:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:57:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:57:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:57:33: 7000000 INFO @ Tue, 02 Aug 2022 14:57:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:57:48: 8000000 INFO @ Tue, 02 Aug 2022 14:57:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:57:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:57:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.10_summits.bed INFO @ Tue, 02 Aug 2022 14:57:50: Done! pass1 - making usageList (288 chroms): 2 millis pass2 - checking and writing primary data (522 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:57:56: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:57:56: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:57:56: #1 total tags in treatment: 8494151 INFO @ Tue, 02 Aug 2022 14:57:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:57:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:57:57: #1 tags after filtering in treatment: 8493953 INFO @ Tue, 02 Aug 2022 14:57:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:57:57: #1 finished! INFO @ Tue, 02 Aug 2022 14:57:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:57:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:57:57: #2 number of paired peaks: 412 WARNING @ Tue, 02 Aug 2022 14:57:57: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 02 Aug 2022 14:57:57: start model_add_line... INFO @ Tue, 02 Aug 2022 14:57:57: start X-correlation... INFO @ Tue, 02 Aug 2022 14:57:57: end of X-cor INFO @ Tue, 02 Aug 2022 14:57:57: #2 finished! INFO @ Tue, 02 Aug 2022 14:57:57: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 14:57:57: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 14:57:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.20_model.r WARNING @ Tue, 02 Aug 2022 14:57:58: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:57:58: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 14:57:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:57:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:57:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:58:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206526/SRX15206526.20_summits.bed INFO @ Tue, 02 Aug 2022 14:58:24: Done! pass1 - making usageList (189 chroms): 2 millis pass2 - checking and writing primary data (284 records, 4 fields): 36 millis CompletedMACS2peakCalling