Job ID = 6627589 SRX = SRX8521349 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: 00:15:32 120803333 reads; of these: 120803333 (100.00%) were unpaired; of these: 106432247 (88.10%) aligned 0 times 11147761 (9.23%) aligned exactly 1 time 3223325 (2.67%) aligned >1 times 11.90% overall alignment rate Time searching: 00:15:32 Overall time: 00:15:32 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] 3640934 / 14371086 = 0.2534 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 12:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.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 12:25:11: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:25:11: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:25:17: 1000000 INFO @ Tue, 14 Jul 2020 12:25:23: 2000000 INFO @ Tue, 14 Jul 2020 12:25:29: 3000000 INFO @ Tue, 14 Jul 2020 12:25:35: 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 12:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.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 12:25:41: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:25:41: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:25:41: 5000000 INFO @ Tue, 14 Jul 2020 12:25:48: 1000000 INFO @ Tue, 14 Jul 2020 12:25:48: 6000000 INFO @ Tue, 14 Jul 2020 12:25:55: 2000000 INFO @ Tue, 14 Jul 2020 12:25:55: 7000000 INFO @ Tue, 14 Jul 2020 12:26:02: 3000000 INFO @ Tue, 14 Jul 2020 12:26:02: 8000000 INFO @ Tue, 14 Jul 2020 12:26:09: 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 12:26:10: 9000000 INFO @ Tue, 14 Jul 2020 12:26:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.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 12:26:11: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:26:11: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:26:16: 5000000 INFO @ Tue, 14 Jul 2020 12:26:18: 10000000 INFO @ Tue, 14 Jul 2020 12:26:19: 1000000 INFO @ Tue, 14 Jul 2020 12:26:24: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:26:24: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:26:24: #1 total tags in treatment: 10730152 INFO @ Tue, 14 Jul 2020 12:26:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:26:24: #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 12:26:24: #1 tags after filtering in treatment: 10730000 INFO @ Tue, 14 Jul 2020 12:26:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:26:24: #1 finished! INFO @ Tue, 14 Jul 2020 12:26:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:26:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:26:24: 6000000 INFO @ Tue, 14 Jul 2020 12:26:25: #2 number of paired peaks: 413 WARNING @ Tue, 14 Jul 2020 12:26:25: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 14 Jul 2020 12:26:25: start model_add_line... INFO @ Tue, 14 Jul 2020 12:26:25: start X-correlation... INFO @ Tue, 14 Jul 2020 12:26:25: end of X-cor INFO @ Tue, 14 Jul 2020 12:26:25: #2 finished! INFO @ Tue, 14 Jul 2020 12:26:25: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 12:26:25: #2 alternative fragment length(s) may be 4,56,563 bps INFO @ Tue, 14 Jul 2020 12:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.05_model.r WARNING @ Tue, 14 Jul 2020 12:26:25: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:26:25: #2 You may need to consider one of the other alternative d(s): 4,56,563 WARNING @ Tue, 14 Jul 2020 12:26:25: #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 12:26:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:26:28: 2000000 INFO @ Tue, 14 Jul 2020 12:26:32: 7000000 INFO @ Tue, 14 Jul 2020 12:26:37: 3000000 INFO @ Tue, 14 Jul 2020 12:26:39: 8000000 INFO @ Tue, 14 Jul 2020 12:26:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:26:45: 4000000 INFO @ Tue, 14 Jul 2020 12:26:47: 9000000 INFO @ Tue, 14 Jul 2020 12:26:54: 5000000 INFO @ Tue, 14 Jul 2020 12:26:55: 10000000 INFO @ Tue, 14 Jul 2020 12:26:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:26:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:26:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.05_summits.bed INFO @ Tue, 14 Jul 2020 12:26:56: Done! pass1 - making usageList (260 chroms): 1 millis pass2 - checking and writing primary data (2356 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:27:01: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:27:01: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:27:01: #1 total tags in treatment: 10730152 INFO @ Tue, 14 Jul 2020 12:27:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:27:01: #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 12:27:01: #1 tags after filtering in treatment: 10730000 INFO @ Tue, 14 Jul 2020 12:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:27:01: #1 finished! INFO @ Tue, 14 Jul 2020 12:27:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:27:02: #2 number of paired peaks: 413 WARNING @ Tue, 14 Jul 2020 12:27:02: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 14 Jul 2020 12:27:02: start model_add_line... INFO @ Tue, 14 Jul 2020 12:27:02: start X-correlation... INFO @ Tue, 14 Jul 2020 12:27:02: end of X-cor INFO @ Tue, 14 Jul 2020 12:27:02: #2 finished! INFO @ Tue, 14 Jul 2020 12:27:02: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 12:27:02: #2 alternative fragment length(s) may be 4,56,563 bps INFO @ Tue, 14 Jul 2020 12:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.10_model.r WARNING @ Tue, 14 Jul 2020 12:27:02: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:27:02: #2 You may need to consider one of the other alternative d(s): 4,56,563 WARNING @ Tue, 14 Jul 2020 12:27:02: #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 12:27:02: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:27:03: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:27:11: 7000000 INFO @ Tue, 14 Jul 2020 12:27:19: 8000000 INFO @ Tue, 14 Jul 2020 12:27:24: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:27:27: 9000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:27:35: 10000000 INFO @ Tue, 14 Jul 2020 12:27:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:27:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:27:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.10_summits.bed INFO @ Tue, 14 Jul 2020 12:27:36: Done! pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:27:41: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:27:41: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:27:41: #1 total tags in treatment: 10730152 INFO @ Tue, 14 Jul 2020 12:27:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:27:41: #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 12:27:41: #1 tags after filtering in treatment: 10730000 INFO @ Tue, 14 Jul 2020 12:27:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:27:41: #1 finished! INFO @ Tue, 14 Jul 2020 12:27:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:27:42: #2 number of paired peaks: 413 WARNING @ Tue, 14 Jul 2020 12:27:42: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 14 Jul 2020 12:27:42: start model_add_line... INFO @ Tue, 14 Jul 2020 12:27:42: start X-correlation... INFO @ Tue, 14 Jul 2020 12:27:42: end of X-cor INFO @ Tue, 14 Jul 2020 12:27:42: #2 finished! INFO @ Tue, 14 Jul 2020 12:27:42: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 12:27:42: #2 alternative fragment length(s) may be 4,56,563 bps INFO @ Tue, 14 Jul 2020 12:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.20_model.r WARNING @ Tue, 14 Jul 2020 12:27:42: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:27:42: #2 You may need to consider one of the other alternative d(s): 4,56,563 WARNING @ Tue, 14 Jul 2020 12:27:42: #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 12:27:42: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:28:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:28:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:28:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:28:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521349/SRX8521349.20_summits.bed INFO @ Tue, 14 Jul 2020 12:28:14: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 4 millis CompletedMACS2peakCalling