Job ID = 14171772 SRX = SRX9986142 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: 00:06:35 24384523 reads; of these: 24384523 (100.00%) were unpaired; of these: 1408580 (5.78%) aligned 0 times 14833152 (60.83%) aligned exactly 1 time 8142791 (33.39%) aligned >1 times 94.22% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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] 4912399 / 22975943 = 0.2138 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:57:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.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 @ Sat, 11 Dec 2021 12:57:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:57:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:57:17: 1000000 INFO @ Sat, 11 Dec 2021 12:57:23: 2000000 INFO @ Sat, 11 Dec 2021 12:57:29: 3000000 INFO @ Sat, 11 Dec 2021 12:57:35: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:57:41: 5000000 INFO @ Sat, 11 Dec 2021 12:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.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 @ Sat, 11 Dec 2021 12:57:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:57:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:57:48: 6000000 INFO @ Sat, 11 Dec 2021 12:57:49: 1000000 INFO @ Sat, 11 Dec 2021 12:57:55: 7000000 INFO @ Sat, 11 Dec 2021 12:57:57: 2000000 INFO @ Sat, 11 Dec 2021 12:58:02: 8000000 INFO @ Sat, 11 Dec 2021 12:58:05: 3000000 INFO @ Sat, 11 Dec 2021 12:58:09: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:58:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.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 @ Sat, 11 Dec 2021 12:58:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:58:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:58:13: 4000000 INFO @ Sat, 11 Dec 2021 12:58:17: 10000000 INFO @ Sat, 11 Dec 2021 12:58:19: 1000000 INFO @ Sat, 11 Dec 2021 12:58:21: 5000000 INFO @ Sat, 11 Dec 2021 12:58:24: 11000000 INFO @ Sat, 11 Dec 2021 12:58:28: 2000000 INFO @ Sat, 11 Dec 2021 12:58:29: 6000000 INFO @ Sat, 11 Dec 2021 12:58:31: 12000000 INFO @ Sat, 11 Dec 2021 12:58:36: 3000000 INFO @ Sat, 11 Dec 2021 12:58:37: 7000000 INFO @ Sat, 11 Dec 2021 12:58:39: 13000000 INFO @ Sat, 11 Dec 2021 12:58:44: 4000000 INFO @ Sat, 11 Dec 2021 12:58:45: 8000000 INFO @ Sat, 11 Dec 2021 12:58:46: 14000000 INFO @ Sat, 11 Dec 2021 12:58:52: 5000000 INFO @ Sat, 11 Dec 2021 12:58:53: 15000000 INFO @ Sat, 11 Dec 2021 12:58:54: 9000000 INFO @ Sat, 11 Dec 2021 12:59:00: 6000000 INFO @ Sat, 11 Dec 2021 12:59:01: 16000000 INFO @ Sat, 11 Dec 2021 12:59:02: 10000000 INFO @ Sat, 11 Dec 2021 12:59:08: 17000000 INFO @ Sat, 11 Dec 2021 12:59:08: 7000000 INFO @ Sat, 11 Dec 2021 12:59:10: 11000000 INFO @ Sat, 11 Dec 2021 12:59:16: 18000000 INFO @ Sat, 11 Dec 2021 12:59:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:59:16: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:59:16: #1 total tags in treatment: 18063544 INFO @ Sat, 11 Dec 2021 12:59:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:59:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:59:17: 8000000 INFO @ Sat, 11 Dec 2021 12:59:17: #1 tags after filtering in treatment: 18063488 INFO @ Sat, 11 Dec 2021 12:59:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:59:17: #1 finished! INFO @ Sat, 11 Dec 2021 12:59:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:59:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:59:18: 12000000 INFO @ Sat, 11 Dec 2021 12:59:18: #2 number of paired peaks: 880 WARNING @ Sat, 11 Dec 2021 12:59:18: Fewer paired peaks (880) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 880 pairs to build model! INFO @ Sat, 11 Dec 2021 12:59:18: start model_add_line... INFO @ Sat, 11 Dec 2021 12:59:18: start X-correlation... INFO @ Sat, 11 Dec 2021 12:59:18: end of X-cor INFO @ Sat, 11 Dec 2021 12:59:18: #2 finished! INFO @ Sat, 11 Dec 2021 12:59:18: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 12:59:18: #2 alternative fragment length(s) may be 2,46,553 bps INFO @ Sat, 11 Dec 2021 12:59:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.05_model.r WARNING @ Sat, 11 Dec 2021 12:59:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:59:18: #2 You may need to consider one of the other alternative d(s): 2,46,553 WARNING @ Sat, 11 Dec 2021 12:59:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:59:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:59:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:59:25: 9000000 INFO @ Sat, 11 Dec 2021 12:59:26: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:59:33: 10000000 INFO @ Sat, 11 Dec 2021 12:59:34: 14000000 INFO @ Sat, 11 Dec 2021 12:59:41: 11000000 INFO @ Sat, 11 Dec 2021 12:59:42: 15000000 INFO @ Sat, 11 Dec 2021 12:59:49: 12000000 INFO @ Sat, 11 Dec 2021 12:59:50: 16000000 INFO @ Sat, 11 Dec 2021 12:59:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:59:57: 13000000 INFO @ Sat, 11 Dec 2021 12:59:58: 17000000 INFO @ Sat, 11 Dec 2021 13:00:05: 14000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:00:05: 18000000 INFO @ Sat, 11 Dec 2021 13:00:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:00:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:00:06: #1 total tags in treatment: 18063544 INFO @ Sat, 11 Dec 2021 13:00:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:00:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:00:07: #1 tags after filtering in treatment: 18063488 INFO @ Sat, 11 Dec 2021 13:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:00:07: #1 finished! INFO @ Sat, 11 Dec 2021 13:00:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:00:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:00:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.05_summits.bed INFO @ Sat, 11 Dec 2021 13:00:07: Done! INFO @ Sat, 11 Dec 2021 13:00:08: #2 number of paired peaks: 880 WARNING @ Sat, 11 Dec 2021 13:00:08: Fewer paired peaks (880) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 880 pairs to build model! INFO @ Sat, 11 Dec 2021 13:00:08: start model_add_line... pass1 - making usageList (638 chroms): 1 millis pass2 - checking and writing primary data (2893 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:00:08: start X-correlation... INFO @ Sat, 11 Dec 2021 13:00:08: end of X-cor INFO @ Sat, 11 Dec 2021 13:00:08: #2 finished! INFO @ Sat, 11 Dec 2021 13:00:08: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 13:00:08: #2 alternative fragment length(s) may be 2,46,553 bps INFO @ Sat, 11 Dec 2021 13:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.10_model.r WARNING @ Sat, 11 Dec 2021 13:00:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:00:08: #2 You may need to consider one of the other alternative d(s): 2,46,553 WARNING @ Sat, 11 Dec 2021 13:00:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:00:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:00:12: 15000000 INFO @ Sat, 11 Dec 2021 13:00:20: 16000000 INFO @ Sat, 11 Dec 2021 13:00:27: 17000000 INFO @ Sat, 11 Dec 2021 13:00:34: 18000000 INFO @ Sat, 11 Dec 2021 13:00:34: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:00:34: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:00:34: #1 total tags in treatment: 18063544 INFO @ Sat, 11 Dec 2021 13:00:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:00:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:00:35: #1 tags after filtering in treatment: 18063488 INFO @ Sat, 11 Dec 2021 13:00:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:00:35: #1 finished! INFO @ Sat, 11 Dec 2021 13:00:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:00:36: #2 number of paired peaks: 880 WARNING @ Sat, 11 Dec 2021 13:00:36: Fewer paired peaks (880) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 880 pairs to build model! INFO @ Sat, 11 Dec 2021 13:00:36: start model_add_line... INFO @ Sat, 11 Dec 2021 13:00:36: start X-correlation... INFO @ Sat, 11 Dec 2021 13:00:36: end of X-cor INFO @ Sat, 11 Dec 2021 13:00:36: #2 finished! INFO @ Sat, 11 Dec 2021 13:00:36: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 13:00:36: #2 alternative fragment length(s) may be 2,46,553 bps INFO @ Sat, 11 Dec 2021 13:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.20_model.r WARNING @ Sat, 11 Dec 2021 13:00:36: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:00:36: #2 You may need to consider one of the other alternative d(s): 2,46,553 WARNING @ Sat, 11 Dec 2021 13:00:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:00:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:00:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.10_summits.bed INFO @ Sat, 11 Dec 2021 13:00:56: Done! pass1 - making usageList (525 chroms): 1 millis pass2 - checking and writing primary data (2086 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:01:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986142/SRX9986142.20_summits.bed INFO @ Sat, 11 Dec 2021 13:01:24: Done! pass1 - making usageList (310 chroms): 1 millis pass2 - checking and writing primary data (710 records, 4 fields): 10 millis CompletedMACS2peakCalling