Job ID = 6529728 SRX = SRX4510348 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: 00:08:31 19656463 reads; of these: 19656463 (100.00%) were unpaired; of these: 1512421 (7.69%) aligned 0 times 15380963 (78.25%) aligned exactly 1 time 2763079 (14.06%) aligned >1 times 92.31% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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] 2115871 / 18144042 = 0.1166 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 02:44:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.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 02:44:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:44:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:44:56: 1000000 INFO @ Tue, 30 Jun 2020 02:45:03: 2000000 INFO @ Tue, 30 Jun 2020 02:45:10: 3000000 INFO @ Tue, 30 Jun 2020 02:45:17: 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 02:45:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.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 02:45:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:25: 5000000 INFO @ Tue, 30 Jun 2020 02:45:29: 1000000 INFO @ Tue, 30 Jun 2020 02:45:35: 6000000 INFO @ Tue, 30 Jun 2020 02:45:39: 2000000 INFO @ Tue, 30 Jun 2020 02:45:44: 7000000 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 02:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.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 02:45:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:49: 3000000 INFO @ Tue, 30 Jun 2020 02:45:53: 8000000 INFO @ Tue, 30 Jun 2020 02:45:59: 1000000 INFO @ Tue, 30 Jun 2020 02:45:59: 4000000 INFO @ Tue, 30 Jun 2020 02:46:02: 9000000 INFO @ Tue, 30 Jun 2020 02:46:08: 2000000 INFO @ Tue, 30 Jun 2020 02:46:09: 5000000 INFO @ Tue, 30 Jun 2020 02:46:12: 10000000 INFO @ Tue, 30 Jun 2020 02:46:17: 3000000 INFO @ Tue, 30 Jun 2020 02:46:19: 6000000 INFO @ Tue, 30 Jun 2020 02:46:21: 11000000 INFO @ Tue, 30 Jun 2020 02:46:27: 4000000 INFO @ Tue, 30 Jun 2020 02:46:29: 7000000 INFO @ Tue, 30 Jun 2020 02:46:31: 12000000 INFO @ Tue, 30 Jun 2020 02:46:36: 5000000 INFO @ Tue, 30 Jun 2020 02:46:39: 8000000 INFO @ Tue, 30 Jun 2020 02:46:40: 13000000 INFO @ Tue, 30 Jun 2020 02:46:45: 6000000 INFO @ Tue, 30 Jun 2020 02:46:49: 9000000 INFO @ Tue, 30 Jun 2020 02:46:50: 14000000 INFO @ Tue, 30 Jun 2020 02:46:55: 7000000 INFO @ Tue, 30 Jun 2020 02:46:59: 15000000 INFO @ Tue, 30 Jun 2020 02:46:59: 10000000 INFO @ Tue, 30 Jun 2020 02:47:04: 8000000 INFO @ Tue, 30 Jun 2020 02:47:09: 16000000 INFO @ Tue, 30 Jun 2020 02:47:09: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:47:09: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:47:09: #1 total tags in treatment: 16028171 INFO @ Tue, 30 Jun 2020 02:47:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:09: #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 02:47:10: #1 tags after filtering in treatment: 16028039 INFO @ Tue, 30 Jun 2020 02:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:10: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:47:11: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 02:47:11: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:11: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:11: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:11: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:11: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:11: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 02:47:11: #2 alternative fragment length(s) may be 4,95,518,544 bps INFO @ Tue, 30 Jun 2020 02:47:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.05_model.r WARNING @ Tue, 30 Jun 2020 02:47:11: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:11: #2 You may need to consider one of the other alternative d(s): 4,95,518,544 WARNING @ Tue, 30 Jun 2020 02:47:11: #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 02:47:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:13: 9000000 INFO @ Tue, 30 Jun 2020 02:47:20: 12000000 INFO @ Tue, 30 Jun 2020 02:47:22: 10000000 INFO @ Tue, 30 Jun 2020 02:47:31: 13000000 INFO @ Tue, 30 Jun 2020 02:47:31: 11000000 INFO @ Tue, 30 Jun 2020 02:47:40: 12000000 INFO @ Tue, 30 Jun 2020 02:47:41: 14000000 INFO @ Tue, 30 Jun 2020 02:47:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:47:50: 13000000 INFO @ Tue, 30 Jun 2020 02:47:51: 15000000 INFO @ Tue, 30 Jun 2020 02:47:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:47:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:47:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.05_summits.bed INFO @ Tue, 30 Jun 2020 02:47:56: Done! pass1 - making usageList (414 chroms): 1 millis pass2 - checking and writing primary data (1186 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:47:59: 14000000 INFO @ Tue, 30 Jun 2020 02:48:01: 16000000 INFO @ Tue, 30 Jun 2020 02:48:01: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:48:01: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:48:01: #1 total tags in treatment: 16028171 INFO @ Tue, 30 Jun 2020 02:48:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:01: #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 02:48:02: #1 tags after filtering in treatment: 16028039 INFO @ Tue, 30 Jun 2020 02:48:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:02: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:03: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 02:48:03: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:03: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:03: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 02:48:03: #2 alternative fragment length(s) may be 4,95,518,544 bps INFO @ Tue, 30 Jun 2020 02:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.10_model.r WARNING @ Tue, 30 Jun 2020 02:48:03: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:03: #2 You may need to consider one of the other alternative d(s): 4,95,518,544 WARNING @ Tue, 30 Jun 2020 02:48:03: #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 02:48:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:07: 15000000 INFO @ Tue, 30 Jun 2020 02:48:15: 16000000 INFO @ Tue, 30 Jun 2020 02:48:16: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:48:16: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:48:16: #1 total tags in treatment: 16028171 INFO @ Tue, 30 Jun 2020 02:48:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:16: #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 02:48:16: #1 tags after filtering in treatment: 16028039 INFO @ Tue, 30 Jun 2020 02:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:16: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:17: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 02:48:17: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:17: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:17: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:17: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:17: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:17: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 02:48:17: #2 alternative fragment length(s) may be 4,95,518,544 bps INFO @ Tue, 30 Jun 2020 02:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.20_model.r WARNING @ Tue, 30 Jun 2020 02:48:17: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:17: #2 You may need to consider one of the other alternative d(s): 4,95,518,544 WARNING @ Tue, 30 Jun 2020 02:48:17: #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 02:48:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.10_summits.bed INFO @ Tue, 30 Jun 2020 02:48:49: Done! pass1 - making usageList (344 chroms): 2 millis pass2 - checking and writing primary data (799 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4510348/SRX4510348.20_summits.bed INFO @ Tue, 30 Jun 2020 02:49:02: Done! pass1 - making usageList (241 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 7 millis CompletedMACS2peakCalling