Job ID = 6529429 SRX = SRX2618527 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: 00:05:21 17140597 reads; of these: 17140597 (100.00%) were unpaired; of these: 869134 (5.07%) aligned 0 times 11368593 (66.33%) aligned exactly 1 time 4902870 (28.60%) aligned >1 times 94.93% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 2431613 / 16271463 = 0.1494 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 02:13:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.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 02:13:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:13:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:03: 1000000 INFO @ Tue, 30 Jun 2020 02:14:09: 2000000 INFO @ Tue, 30 Jun 2020 02:14:14: 3000000 INFO @ Tue, 30 Jun 2020 02:14:19: 4000000 INFO @ Tue, 30 Jun 2020 02:14:25: 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 02:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.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 02:14:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:30: 6000000 INFO @ Tue, 30 Jun 2020 02:14:34: 1000000 INFO @ Tue, 30 Jun 2020 02:14:36: 7000000 INFO @ Tue, 30 Jun 2020 02:14:40: 2000000 INFO @ Tue, 30 Jun 2020 02:14:41: 8000000 INFO @ Tue, 30 Jun 2020 02:14:46: 3000000 INFO @ Tue, 30 Jun 2020 02:14:47: 9000000 INFO @ Tue, 30 Jun 2020 02:14:51: 4000000 INFO @ Tue, 30 Jun 2020 02:14:53: 10000000 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 02:14:57: 5000000 INFO @ Tue, 30 Jun 2020 02:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.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 02:14:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:59: 11000000 INFO @ Tue, 30 Jun 2020 02:15:03: 6000000 INFO @ Tue, 30 Jun 2020 02:15:04: 1000000 INFO @ Tue, 30 Jun 2020 02:15:05: 12000000 INFO @ Tue, 30 Jun 2020 02:15:09: 7000000 INFO @ Tue, 30 Jun 2020 02:15:10: 2000000 INFO @ Tue, 30 Jun 2020 02:15:11: 13000000 INFO @ Tue, 30 Jun 2020 02:15:14: 8000000 INFO @ Tue, 30 Jun 2020 02:15:16: 3000000 INFO @ Tue, 30 Jun 2020 02:15:16: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:16: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:16: #1 total tags in treatment: 13839850 INFO @ Tue, 30 Jun 2020 02:15:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:16: #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 02:15:17: #1 tags after filtering in treatment: 13839850 INFO @ Tue, 30 Jun 2020 02:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:18: #2 number of paired peaks: 818 WARNING @ Tue, 30 Jun 2020 02:15:18: Fewer paired peaks (818) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 818 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:18: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:15:18: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 02:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.05_model.r WARNING @ Tue, 30 Jun 2020 02:15:18: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:18: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 02:15:18: #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 02:15:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:20: 9000000 INFO @ Tue, 30 Jun 2020 02:15:21: 4000000 INFO @ Tue, 30 Jun 2020 02:15:26: 10000000 INFO @ Tue, 30 Jun 2020 02:15:27: 5000000 INFO @ Tue, 30 Jun 2020 02:15:32: 11000000 INFO @ Tue, 30 Jun 2020 02:15:33: 6000000 INFO @ Tue, 30 Jun 2020 02:15:38: 12000000 INFO @ Tue, 30 Jun 2020 02:15:39: 7000000 INFO @ Tue, 30 Jun 2020 02:15:44: 13000000 INFO @ Tue, 30 Jun 2020 02:15:44: 8000000 INFO @ Tue, 30 Jun 2020 02:15:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:15:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:50: #1 total tags in treatment: 13839850 INFO @ Tue, 30 Jun 2020 02:15:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:50: #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 02:15:50: 9000000 INFO @ Tue, 30 Jun 2020 02:15:50: #1 tags after filtering in treatment: 13839850 INFO @ Tue, 30 Jun 2020 02:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:51: #2 number of paired peaks: 818 WARNING @ Tue, 30 Jun 2020 02:15:51: Fewer paired peaks (818) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 818 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:51: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:15:51: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 02:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.10_model.r WARNING @ Tue, 30 Jun 2020 02:15:51: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:51: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 02:15:51: #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 02:15:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:56: 10000000 INFO @ Tue, 30 Jun 2020 02:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.05_summits.bed INFO @ Tue, 30 Jun 2020 02:16:01: Done! pass1 - making usageList (637 chroms): 2 millis pass2 - checking and writing primary data (2162 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:02: 11000000 INFO @ Tue, 30 Jun 2020 02:16:08: 12000000 INFO @ Tue, 30 Jun 2020 02:16:14: 13000000 INFO @ Tue, 30 Jun 2020 02:16:19: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:16:19: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:16:19: #1 total tags in treatment: 13839850 INFO @ Tue, 30 Jun 2020 02:16:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:16:19: #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 02:16:19: #1 tags after filtering in treatment: 13839850 INFO @ Tue, 30 Jun 2020 02:16:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:16:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:16:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:16:19: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:16:20: #2 number of paired peaks: 818 WARNING @ Tue, 30 Jun 2020 02:16:20: Fewer paired peaks (818) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 818 pairs to build model! INFO @ Tue, 30 Jun 2020 02:16:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:16:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:16:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:16:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:16:20: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:16:20: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 02:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.20_model.r WARNING @ Tue, 30 Jun 2020 02:16:20: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:16:20: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 02:16:20: #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 02:16:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:16:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.10_summits.bed INFO @ Tue, 30 Jun 2020 02:16:35: Done! pass1 - making usageList (522 chroms): 2 millis pass2 - checking and writing primary data (1921 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:17:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:17:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:17:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618527/SRX2618527.20_summits.bed INFO @ Tue, 30 Jun 2020 02:17:04: Done! pass1 - making usageList (424 chroms): 1 millis pass2 - checking and writing primary data (1261 records, 4 fields): 14 millis CompletedMACS2peakCalling