Job ID = 6529235 SRX = SRX1084158 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: 00:04:45 21976820 reads; of these: 21976820 (100.00%) were unpaired; of these: 2242319 (10.20%) aligned 0 times 15912001 (72.40%) aligned exactly 1 time 3822500 (17.39%) aligned >1 times 89.80% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 2404120 / 19734501 = 0.1218 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 01:42:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.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 01:42:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:42:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:42:12: 1000000 INFO @ Tue, 30 Jun 2020 01:42:19: 2000000 INFO @ Tue, 30 Jun 2020 01:42:25: 3000000 INFO @ Tue, 30 Jun 2020 01:42:32: 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, 30 Jun 2020 01:42:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.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 01:42:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:42:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:42:39: 5000000 INFO @ Tue, 30 Jun 2020 01:42:42: 1000000 INFO @ Tue, 30 Jun 2020 01:42:46: 6000000 INFO @ Tue, 30 Jun 2020 01:42:50: 2000000 INFO @ Tue, 30 Jun 2020 01:42:54: 7000000 INFO @ Tue, 30 Jun 2020 01:42:58: 3000000 INFO @ Tue, 30 Jun 2020 01:43:02: 8000000 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 01:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.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 01:43:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:43:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:43:06: 4000000 INFO @ Tue, 30 Jun 2020 01:43:10: 9000000 INFO @ Tue, 30 Jun 2020 01:43:12: 1000000 INFO @ Tue, 30 Jun 2020 01:43:14: 5000000 INFO @ Tue, 30 Jun 2020 01:43:18: 10000000 INFO @ Tue, 30 Jun 2020 01:43:20: 2000000 INFO @ Tue, 30 Jun 2020 01:43:22: 6000000 INFO @ Tue, 30 Jun 2020 01:43:26: 11000000 INFO @ Tue, 30 Jun 2020 01:43:27: 3000000 INFO @ Tue, 30 Jun 2020 01:43:30: 7000000 INFO @ Tue, 30 Jun 2020 01:43:34: 12000000 INFO @ Tue, 30 Jun 2020 01:43:34: 4000000 INFO @ Tue, 30 Jun 2020 01:43:38: 8000000 INFO @ Tue, 30 Jun 2020 01:43:41: 5000000 INFO @ Tue, 30 Jun 2020 01:43:42: 13000000 INFO @ Tue, 30 Jun 2020 01:43:47: 9000000 INFO @ Tue, 30 Jun 2020 01:43:49: 6000000 INFO @ Tue, 30 Jun 2020 01:43:50: 14000000 INFO @ Tue, 30 Jun 2020 01:43:55: 10000000 INFO @ Tue, 30 Jun 2020 01:43:56: 7000000 INFO @ Tue, 30 Jun 2020 01:43:58: 15000000 INFO @ Tue, 30 Jun 2020 01:44:03: 11000000 INFO @ Tue, 30 Jun 2020 01:44:03: 8000000 INFO @ Tue, 30 Jun 2020 01:44:06: 16000000 INFO @ Tue, 30 Jun 2020 01:44:11: 9000000 INFO @ Tue, 30 Jun 2020 01:44:12: 12000000 INFO @ Tue, 30 Jun 2020 01:44:14: 17000000 INFO @ Tue, 30 Jun 2020 01:44:16: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:44:16: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:44:16: #1 total tags in treatment: 17330381 INFO @ Tue, 30 Jun 2020 01:44:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:44:16: #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 01:44:17: #1 tags after filtering in treatment: 17330290 INFO @ Tue, 30 Jun 2020 01:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:44:17: #1 finished! INFO @ Tue, 30 Jun 2020 01:44:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:44:18: #2 number of paired peaks: 256 WARNING @ Tue, 30 Jun 2020 01:44:18: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 30 Jun 2020 01:44:18: start model_add_line... INFO @ Tue, 30 Jun 2020 01:44:18: 10000000 INFO @ Tue, 30 Jun 2020 01:44:18: start X-correlation... INFO @ Tue, 30 Jun 2020 01:44:18: end of X-cor INFO @ Tue, 30 Jun 2020 01:44:18: #2 finished! INFO @ Tue, 30 Jun 2020 01:44:18: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 01:44:18: #2 alternative fragment length(s) may be 3,47,557 bps INFO @ Tue, 30 Jun 2020 01:44:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.05_model.r WARNING @ Tue, 30 Jun 2020 01:44:18: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:44:18: #2 You may need to consider one of the other alternative d(s): 3,47,557 WARNING @ Tue, 30 Jun 2020 01:44:18: #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 01:44:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:44:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:44:20: 13000000 INFO @ Tue, 30 Jun 2020 01:44:25: 11000000 INFO @ Tue, 30 Jun 2020 01:44:28: 14000000 INFO @ Tue, 30 Jun 2020 01:44:32: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:44:36: 15000000 INFO @ Tue, 30 Jun 2020 01:44:40: 13000000 INFO @ Tue, 30 Jun 2020 01:44:44: 16000000 INFO @ Tue, 30 Jun 2020 01:44:47: 14000000 INFO @ Tue, 30 Jun 2020 01:44:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:44:52: 17000000 INFO @ Tue, 30 Jun 2020 01:44:55: 15000000 INFO @ Tue, 30 Jun 2020 01:44:55: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:44:55: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:44:55: #1 total tags in treatment: 17330381 INFO @ Tue, 30 Jun 2020 01:44:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:44:55: #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 01:44:55: #1 tags after filtering in treatment: 17330290 INFO @ Tue, 30 Jun 2020 01:44:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:44:55: #1 finished! INFO @ Tue, 30 Jun 2020 01:44:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:44:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:44:56: #2 number of paired peaks: 256 WARNING @ Tue, 30 Jun 2020 01:44:56: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 30 Jun 2020 01:44:56: start model_add_line... INFO @ Tue, 30 Jun 2020 01:44:56: start X-correlation... INFO @ Tue, 30 Jun 2020 01:44:57: end of X-cor INFO @ Tue, 30 Jun 2020 01:44:57: #2 finished! INFO @ Tue, 30 Jun 2020 01:44:57: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 01:44:57: #2 alternative fragment length(s) may be 3,47,557 bps INFO @ Tue, 30 Jun 2020 01:44:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.10_model.r WARNING @ Tue, 30 Jun 2020 01:44:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:44:57: #2 You may need to consider one of the other alternative d(s): 3,47,557 WARNING @ Tue, 30 Jun 2020 01:44:57: #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 01:44:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:45:01: 16000000 INFO @ Tue, 30 Jun 2020 01:45:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:45:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:45:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.05_summits.bed INFO @ Tue, 30 Jun 2020 01:45:05: Done! pass1 - making usageList (566 chroms): 1 millis pass2 - checking and writing primary data (3840 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:45:08: 17000000 INFO @ Tue, 30 Jun 2020 01:45:10: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:45:10: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:45:10: #1 total tags in treatment: 17330381 INFO @ Tue, 30 Jun 2020 01:45:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:45:10: #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 01:45:11: #1 tags after filtering in treatment: 17330290 INFO @ Tue, 30 Jun 2020 01:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:45:11: #1 finished! INFO @ Tue, 30 Jun 2020 01:45:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:45:11: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:45:12: #2 number of paired peaks: 256 WARNING @ Tue, 30 Jun 2020 01:45:12: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 30 Jun 2020 01:45:12: start model_add_line... INFO @ Tue, 30 Jun 2020 01:45:12: start X-correlation... INFO @ Tue, 30 Jun 2020 01:45:12: end of X-cor INFO @ Tue, 30 Jun 2020 01:45:12: #2 finished! INFO @ Tue, 30 Jun 2020 01:45:12: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 01:45:12: #2 alternative fragment length(s) may be 3,47,557 bps INFO @ Tue, 30 Jun 2020 01:45:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.20_model.r WARNING @ Tue, 30 Jun 2020 01:45:12: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:45:12: #2 You may need to consider one of the other alternative d(s): 3,47,557 WARNING @ Tue, 30 Jun 2020 01:45:12: #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 01:45:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:45:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.10_summits.bed INFO @ Tue, 30 Jun 2020 01:45:43: Done! pass1 - making usageList (485 chroms): 1 millis pass2 - checking and writing primary data (1896 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:45:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084158/SRX1084158.20_summits.bed INFO @ Tue, 30 Jun 2020 01:45:59: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 7 millis CompletedMACS2peakCalling