Job ID = 6529488 SRX = SRX287787 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:28 18858986 reads; of these: 18858986 (100.00%) were unpaired; of these: 1147280 (6.08%) aligned 0 times 14292879 (75.79%) aligned exactly 1 time 3418827 (18.13%) aligned >1 times 93.92% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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 8 files... [bam_rmdupse_core] 2033104 / 17711706 = 0.1148 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, 30 Jun 2020 02:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.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, 30 Jun 2020 02:32:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:22: 1000000 INFO @ Tue, 30 Jun 2020 02:32:27: 2000000 INFO @ Tue, 30 Jun 2020 02:32:33: 3000000 INFO @ Tue, 30 Jun 2020 02:32:38: 4000000 INFO @ Tue, 30 Jun 2020 02:32:44: 5000000 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, 30 Jun 2020 02:32:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.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, 30 Jun 2020 02:32:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:50: 6000000 INFO @ Tue, 30 Jun 2020 02:32:54: 1000000 INFO @ Tue, 30 Jun 2020 02:32:56: 7000000 INFO @ Tue, 30 Jun 2020 02:33:01: 2000000 INFO @ Tue, 30 Jun 2020 02:33:03: 8000000 INFO @ Tue, 30 Jun 2020 02:33:07: 3000000 INFO @ Tue, 30 Jun 2020 02:33:09: 9000000 INFO @ Tue, 30 Jun 2020 02:33:14: 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, 30 Jun 2020 02:33:16: 10000000 INFO @ Tue, 30 Jun 2020 02:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.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, 30 Jun 2020 02:33:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:21: 5000000 INFO @ Tue, 30 Jun 2020 02:33:23: 11000000 INFO @ Tue, 30 Jun 2020 02:33:24: 1000000 INFO @ Tue, 30 Jun 2020 02:33:28: 6000000 INFO @ Tue, 30 Jun 2020 02:33:30: 12000000 INFO @ Tue, 30 Jun 2020 02:33:31: 2000000 INFO @ Tue, 30 Jun 2020 02:33:35: 7000000 INFO @ Tue, 30 Jun 2020 02:33:37: 13000000 INFO @ Tue, 30 Jun 2020 02:33:39: 3000000 INFO @ Tue, 30 Jun 2020 02:33:42: 8000000 INFO @ Tue, 30 Jun 2020 02:33:44: 14000000 INFO @ Tue, 30 Jun 2020 02:33:47: 4000000 INFO @ Tue, 30 Jun 2020 02:33:49: 9000000 INFO @ Tue, 30 Jun 2020 02:33:51: 15000000 INFO @ Tue, 30 Jun 2020 02:33:54: 5000000 INFO @ Tue, 30 Jun 2020 02:33:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:33:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:33:56: #1 total tags in treatment: 15678602 INFO @ Tue, 30 Jun 2020 02:33:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:33:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:33:56: 10000000 INFO @ Tue, 30 Jun 2020 02:33:57: #1 tags after filtering in treatment: 15678601 INFO @ Tue, 30 Jun 2020 02:33:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:33:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:33:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:33:58: #2 number of paired peaks: 116 WARNING @ Tue, 30 Jun 2020 02:33:58: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 30 Jun 2020 02:33:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:33:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:33:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:33:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:33:58: #2 predicted fragment length is 56 bps INFO @ Tue, 30 Jun 2020 02:33:58: #2 alternative fragment length(s) may be 3,56 bps INFO @ Tue, 30 Jun 2020 02:33:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.05_model.r WARNING @ Tue, 30 Jun 2020 02:33:58: #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, 30 Jun 2020 02:33:58: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Tue, 30 Jun 2020 02:33:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:33:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:02: 6000000 INFO @ Tue, 30 Jun 2020 02:34:03: 11000000 INFO @ Tue, 30 Jun 2020 02:34:09: 7000000 INFO @ Tue, 30 Jun 2020 02:34:10: 12000000 INFO @ Tue, 30 Jun 2020 02:34:17: 8000000 INFO @ Tue, 30 Jun 2020 02:34:17: 13000000 INFO @ Tue, 30 Jun 2020 02:34:24: 9000000 INFO @ Tue, 30 Jun 2020 02:34:24: 14000000 INFO @ Tue, 30 Jun 2020 02:34:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:31: 10000000 INFO @ Tue, 30 Jun 2020 02:34:32: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:34:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:34:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:34:37: #1 total tags in treatment: 15678602 INFO @ Tue, 30 Jun 2020 02:34:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:34:37: #1 tags after filtering in treatment: 15678601 INFO @ Tue, 30 Jun 2020 02:34:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:37: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:38: #2 number of paired peaks: 116 WARNING @ Tue, 30 Jun 2020 02:34:38: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:38: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:38: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:38: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:38: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:38: #2 predicted fragment length is 56 bps INFO @ Tue, 30 Jun 2020 02:34:38: #2 alternative fragment length(s) may be 3,56 bps INFO @ Tue, 30 Jun 2020 02:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.10_model.r WARNING @ Tue, 30 Jun 2020 02:34:38: #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, 30 Jun 2020 02:34:38: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Tue, 30 Jun 2020 02:34:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:34:38: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:39: 11000000 INFO @ Tue, 30 Jun 2020 02:34:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:34:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:34:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.05_summits.bed INFO @ Tue, 30 Jun 2020 02:34:39: Done! pass1 - making usageList (388 chroms): 1 millis pass2 - checking and writing primary data (1073 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:34:46: 12000000 INFO @ Tue, 30 Jun 2020 02:34:53: 13000000 INFO @ Tue, 30 Jun 2020 02:35:00: 14000000 INFO @ Tue, 30 Jun 2020 02:35:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:07: 15000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:35:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:35:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:35:11: #1 total tags in treatment: 15678602 INFO @ Tue, 30 Jun 2020 02:35:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:35:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:35:12: #1 tags after filtering in treatment: 15678601 INFO @ Tue, 30 Jun 2020 02:35:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:35:12: #1 finished! INFO @ Tue, 30 Jun 2020 02:35:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:35:13: #2 number of paired peaks: 116 WARNING @ Tue, 30 Jun 2020 02:35:13: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 30 Jun 2020 02:35:13: start model_add_line... INFO @ Tue, 30 Jun 2020 02:35:13: start X-correlation... INFO @ Tue, 30 Jun 2020 02:35:13: end of X-cor INFO @ Tue, 30 Jun 2020 02:35:13: #2 finished! INFO @ Tue, 30 Jun 2020 02:35:13: #2 predicted fragment length is 56 bps INFO @ Tue, 30 Jun 2020 02:35:13: #2 alternative fragment length(s) may be 3,56 bps INFO @ Tue, 30 Jun 2020 02:35:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.20_model.r WARNING @ Tue, 30 Jun 2020 02:35:13: #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, 30 Jun 2020 02:35:13: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Tue, 30 Jun 2020 02:35:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:35:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:35:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.10_summits.bed INFO @ Tue, 30 Jun 2020 02:35:20: Done! pass1 - making usageList (215 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:35:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287787/SRX287787.20_summits.bed INFO @ Tue, 30 Jun 2020 02:35:55: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 4 millis CompletedMACS2peakCalling