Job ID = 6529587 SRX = SRX331375 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: 00:06:10 22948262 reads; of these: 22948262 (100.00%) were unpaired; of these: 1591154 (6.93%) aligned 0 times 16648171 (72.55%) aligned exactly 1 time 4708937 (20.52%) aligned >1 times 93.07% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 5266563 / 21357108 = 0.2466 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 02:24:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.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 02:24:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:16: 1000000 INFO @ Tue, 30 Jun 2020 02:24:21: 2000000 INFO @ Tue, 30 Jun 2020 02:24:27: 3000000 INFO @ Tue, 30 Jun 2020 02:24:33: 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 02:24:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.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 02:24:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:40: 5000000 INFO @ Tue, 30 Jun 2020 02:24:46: 1000000 INFO @ Tue, 30 Jun 2020 02:24:47: 6000000 INFO @ Tue, 30 Jun 2020 02:24:53: 2000000 INFO @ Tue, 30 Jun 2020 02:24:53: 7000000 INFO @ Tue, 30 Jun 2020 02:25:00: 3000000 INFO @ Tue, 30 Jun 2020 02:25:00: 8000000 INFO @ Tue, 30 Jun 2020 02:25:07: 4000000 INFO @ Tue, 30 Jun 2020 02:25:07: 9000000 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 02:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.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 02:25:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:25:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:25:13: 10000000 INFO @ Tue, 30 Jun 2020 02:25:14: 5000000 INFO @ Tue, 30 Jun 2020 02:25:16: 1000000 INFO @ Tue, 30 Jun 2020 02:25:20: 11000000 INFO @ Tue, 30 Jun 2020 02:25:20: 6000000 INFO @ Tue, 30 Jun 2020 02:25:24: 2000000 INFO @ Tue, 30 Jun 2020 02:25:27: 12000000 INFO @ Tue, 30 Jun 2020 02:25:27: 7000000 INFO @ Tue, 30 Jun 2020 02:25:30: 3000000 INFO @ Tue, 30 Jun 2020 02:25:34: 8000000 INFO @ Tue, 30 Jun 2020 02:25:35: 13000000 INFO @ Tue, 30 Jun 2020 02:25:38: 4000000 INFO @ Tue, 30 Jun 2020 02:25:42: 9000000 INFO @ Tue, 30 Jun 2020 02:25:42: 14000000 INFO @ Tue, 30 Jun 2020 02:25:45: 5000000 INFO @ Tue, 30 Jun 2020 02:25:49: 10000000 INFO @ Tue, 30 Jun 2020 02:25:49: 15000000 INFO @ Tue, 30 Jun 2020 02:25:52: 6000000 INFO @ Tue, 30 Jun 2020 02:25:56: 11000000 INFO @ Tue, 30 Jun 2020 02:25:56: 16000000 INFO @ Tue, 30 Jun 2020 02:25:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:25:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:25:57: #1 total tags in treatment: 16090545 INFO @ Tue, 30 Jun 2020 02:25:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:57: #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 02:25:58: #1 tags after filtering in treatment: 16090545 INFO @ Tue, 30 Jun 2020 02:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:59: 7000000 INFO @ Tue, 30 Jun 2020 02:25:59: #2 number of paired peaks: 543 WARNING @ Tue, 30 Jun 2020 02:25:59: Fewer paired peaks (543) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 543 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:59: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:59: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:59: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:59: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:59: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 02:25:59: #2 alternative fragment length(s) may be 3,57,578 bps INFO @ Tue, 30 Jun 2020 02:25:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.05_model.r WARNING @ Tue, 30 Jun 2020 02:25:59: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:25:59: #2 You may need to consider one of the other alternative d(s): 3,57,578 WARNING @ Tue, 30 Jun 2020 02:25:59: #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 02:25:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:26:03: 12000000 INFO @ Tue, 30 Jun 2020 02:26:06: 8000000 INFO @ Tue, 30 Jun 2020 02:26:11: 13000000 INFO @ Tue, 30 Jun 2020 02:26:13: 9000000 INFO @ Tue, 30 Jun 2020 02:26:18: 14000000 INFO @ Tue, 30 Jun 2020 02:26:21: 10000000 INFO @ Tue, 30 Jun 2020 02:26:26: 15000000 INFO @ Tue, 30 Jun 2020 02:26:28: 11000000 INFO @ Tue, 30 Jun 2020 02:26:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:33: 16000000 INFO @ Tue, 30 Jun 2020 02:26:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:26:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:26:34: #1 total tags in treatment: 16090545 INFO @ Tue, 30 Jun 2020 02:26:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:26:34: #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 02:26:35: #1 tags after filtering in treatment: 16090545 INFO @ Tue, 30 Jun 2020 02:26:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:26:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:26:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:26:35: 12000000 INFO @ Tue, 30 Jun 2020 02:26:36: #2 number of paired peaks: 543 WARNING @ Tue, 30 Jun 2020 02:26:36: Fewer paired peaks (543) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 543 pairs to build model! INFO @ Tue, 30 Jun 2020 02:26:36: start model_add_line... INFO @ Tue, 30 Jun 2020 02:26:36: start X-correlation... INFO @ Tue, 30 Jun 2020 02:26:36: end of X-cor INFO @ Tue, 30 Jun 2020 02:26:36: #2 finished! INFO @ Tue, 30 Jun 2020 02:26:36: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 02:26:36: #2 alternative fragment length(s) may be 3,57,578 bps INFO @ Tue, 30 Jun 2020 02:26:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.10_model.r WARNING @ Tue, 30 Jun 2020 02:26:36: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:26:36: #2 You may need to consider one of the other alternative d(s): 3,57,578 WARNING @ Tue, 30 Jun 2020 02:26:36: #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 02:26:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:26:36: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:26:43: 13000000 INFO @ Tue, 30 Jun 2020 02:26:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:26:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:26:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.05_summits.bed INFO @ Tue, 30 Jun 2020 02:26:47: Done! pass1 - making usageList (605 chroms): 2 millis pass2 - checking and writing primary data (2217 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:26:50: 14000000 INFO @ Tue, 30 Jun 2020 02:26:57: 15000000 INFO @ Tue, 30 Jun 2020 02:27:05: 16000000 INFO @ Tue, 30 Jun 2020 02:27:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:27:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:27:06: #1 total tags in treatment: 16090545 INFO @ Tue, 30 Jun 2020 02:27:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:27:06: #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 02:27:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:27:07: #1 tags after filtering in treatment: 16090545 INFO @ Tue, 30 Jun 2020 02:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:27:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:27:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:08: #2 number of paired peaks: 543 WARNING @ Tue, 30 Jun 2020 02:27:08: Fewer paired peaks (543) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 543 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:08: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 02:27:08: #2 alternative fragment length(s) may be 3,57,578 bps INFO @ Tue, 30 Jun 2020 02:27:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.20_model.r WARNING @ Tue, 30 Jun 2020 02:27:08: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:27:08: #2 You may need to consider one of the other alternative d(s): 3,57,578 WARNING @ Tue, 30 Jun 2020 02:27:08: #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 02:27:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.10_summits.bed INFO @ Tue, 30 Jun 2020 02:27:23: Done! pass1 - making usageList (477 chroms): 1 millis pass2 - checking and writing primary data (1713 records, 4 fields): 28 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:27:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:27:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331375/SRX331375.20_summits.bed INFO @ Tue, 30 Jun 2020 02:27:54: Done! pass1 - making usageList (338 chroms): 2 millis pass2 - checking and writing primary data (796 records, 4 fields): 20 millis CompletedMACS2peakCalling