Job ID = 14167396 SRX = SRX9717948 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: 00:15:59 57669504 reads; of these: 57669504 (100.00%) were unpaired; of these: 12079294 (20.95%) aligned 0 times 34413970 (59.67%) aligned exactly 1 time 11176240 (19.38%) aligned >1 times 79.05% overall alignment rate Time searching: 00:15:59 Overall time: 00:15:59 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 20 files... [bam_rmdupse_core] 23993566 / 45590210 = 0.5263 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 @ Fri, 10 Dec 2021 12:32:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.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 @ Fri, 10 Dec 2021 12:32:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:32:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:32:38: 1000000 INFO @ Fri, 10 Dec 2021 12:32:43: 2000000 INFO @ Fri, 10 Dec 2021 12:32:48: 3000000 INFO @ Fri, 10 Dec 2021 12:32:52: 4000000 INFO @ Fri, 10 Dec 2021 12:32:57: 5000000 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 @ Fri, 10 Dec 2021 12:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.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 @ Fri, 10 Dec 2021 12:33:04: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:33:04: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:33:06: 6000000 INFO @ Fri, 10 Dec 2021 12:33:10: 1000000 INFO @ Fri, 10 Dec 2021 12:33:16: 7000000 INFO @ Fri, 10 Dec 2021 12:33:17: 2000000 INFO @ Fri, 10 Dec 2021 12:33:23: 8000000 INFO @ Fri, 10 Dec 2021 12:33:25: 3000000 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 @ Fri, 10 Dec 2021 12:33:32: 4000000 INFO @ Fri, 10 Dec 2021 12:33:33: 9000000 INFO @ Fri, 10 Dec 2021 12:33:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.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 @ Fri, 10 Dec 2021 12:33:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:33:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:33:40: 5000000 INFO @ Fri, 10 Dec 2021 12:33:42: 10000000 INFO @ Fri, 10 Dec 2021 12:33:44: 1000000 INFO @ Fri, 10 Dec 2021 12:33:48: 6000000 INFO @ Fri, 10 Dec 2021 12:33:50: 11000000 INFO @ Fri, 10 Dec 2021 12:33:52: 2000000 INFO @ Fri, 10 Dec 2021 12:33:56: 7000000 INFO @ Fri, 10 Dec 2021 12:33:58: 12000000 INFO @ Fri, 10 Dec 2021 12:34:00: 3000000 INFO @ Fri, 10 Dec 2021 12:34:07: 8000000 INFO @ Fri, 10 Dec 2021 12:34:08: 13000000 INFO @ Fri, 10 Dec 2021 12:34:08: 4000000 INFO @ Fri, 10 Dec 2021 12:34:15: 9000000 INFO @ Fri, 10 Dec 2021 12:34:16: 14000000 INFO @ Fri, 10 Dec 2021 12:34:17: 5000000 INFO @ Fri, 10 Dec 2021 12:34:23: 10000000 INFO @ Fri, 10 Dec 2021 12:34:23: 15000000 INFO @ Fri, 10 Dec 2021 12:34:24: 6000000 INFO @ Fri, 10 Dec 2021 12:34:31: 16000000 INFO @ Fri, 10 Dec 2021 12:34:31: 11000000 INFO @ Fri, 10 Dec 2021 12:34:31: 7000000 INFO @ Fri, 10 Dec 2021 12:34:37: 17000000 INFO @ Fri, 10 Dec 2021 12:34:39: 12000000 INFO @ Fri, 10 Dec 2021 12:34:39: 8000000 INFO @ Fri, 10 Dec 2021 12:34:46: 18000000 INFO @ Fri, 10 Dec 2021 12:34:46: 13000000 INFO @ Fri, 10 Dec 2021 12:34:47: 9000000 INFO @ Fri, 10 Dec 2021 12:34:54: 19000000 INFO @ Fri, 10 Dec 2021 12:34:54: 10000000 INFO @ Fri, 10 Dec 2021 12:34:55: 14000000 INFO @ Fri, 10 Dec 2021 12:35:00: 20000000 INFO @ Fri, 10 Dec 2021 12:35:03: 15000000 INFO @ Fri, 10 Dec 2021 12:35:04: 11000000 INFO @ Fri, 10 Dec 2021 12:35:07: 21000000 INFO @ Fri, 10 Dec 2021 12:35:11: 16000000 INFO @ Fri, 10 Dec 2021 12:35:13: 12000000 INFO @ Fri, 10 Dec 2021 12:35:14: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:35:14: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:35:14: #1 total tags in treatment: 21596644 INFO @ Fri, 10 Dec 2021 12:35:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:35:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:35:15: #1 tags after filtering in treatment: 21596644 INFO @ Fri, 10 Dec 2021 12:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:35:15: #1 finished! INFO @ Fri, 10 Dec 2021 12:35:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:35:16: #2 number of paired peaks: 122 WARNING @ Fri, 10 Dec 2021 12:35:16: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Fri, 10 Dec 2021 12:35:16: start model_add_line... INFO @ Fri, 10 Dec 2021 12:35:17: start X-correlation... INFO @ Fri, 10 Dec 2021 12:35:17: end of X-cor INFO @ Fri, 10 Dec 2021 12:35:17: #2 finished! INFO @ Fri, 10 Dec 2021 12:35:17: #2 predicted fragment length is 41 bps INFO @ Fri, 10 Dec 2021 12:35:17: #2 alternative fragment length(s) may be 3,12,41 bps INFO @ Fri, 10 Dec 2021 12:35:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.05_model.r WARNING @ Fri, 10 Dec 2021 12:35:17: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:35:17: #2 You may need to consider one of the other alternative d(s): 3,12,41 WARNING @ Fri, 10 Dec 2021 12:35:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:35:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:35:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:35:18: 17000000 INFO @ Fri, 10 Dec 2021 12:35:21: 13000000 INFO @ Fri, 10 Dec 2021 12:35:28: 18000000 INFO @ Fri, 10 Dec 2021 12:35:30: 14000000 INFO @ Fri, 10 Dec 2021 12:35:35: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:35:37: 15000000 INFO @ Fri, 10 Dec 2021 12:35:42: 20000000 INFO @ Fri, 10 Dec 2021 12:35:43: 16000000 INFO @ Fri, 10 Dec 2021 12:35:50: 17000000 INFO @ Fri, 10 Dec 2021 12:35:50: 21000000 INFO @ Fri, 10 Dec 2021 12:35:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:35:55: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:35:55: #1 total tags in treatment: 21596644 INFO @ Fri, 10 Dec 2021 12:35:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:35:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:35:56: #1 tags after filtering in treatment: 21596644 INFO @ Fri, 10 Dec 2021 12:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:35:56: #1 finished! INFO @ Fri, 10 Dec 2021 12:35:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:35:57: 18000000 INFO @ Fri, 10 Dec 2021 12:35:57: #2 number of paired peaks: 122 WARNING @ Fri, 10 Dec 2021 12:35:57: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Fri, 10 Dec 2021 12:35:57: start model_add_line... INFO @ Fri, 10 Dec 2021 12:35:58: start X-correlation... INFO @ Fri, 10 Dec 2021 12:35:58: end of X-cor INFO @ Fri, 10 Dec 2021 12:35:58: #2 finished! INFO @ Fri, 10 Dec 2021 12:35:58: #2 predicted fragment length is 41 bps INFO @ Fri, 10 Dec 2021 12:35:58: #2 alternative fragment length(s) may be 3,12,41 bps INFO @ Fri, 10 Dec 2021 12:35:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.10_model.r WARNING @ Fri, 10 Dec 2021 12:35:58: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:35:58: #2 You may need to consider one of the other alternative d(s): 3,12,41 WARNING @ Fri, 10 Dec 2021 12:35:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:35:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:35:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:36:04: 19000000 INFO @ Fri, 10 Dec 2021 12:36:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:36:12: 20000000 INFO @ Fri, 10 Dec 2021 12:36:21: 21000000 INFO @ Fri, 10 Dec 2021 12:36:26: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:36:26: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:36:26: #1 total tags in treatment: 21596644 INFO @ Fri, 10 Dec 2021 12:36:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:36:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:36:27: #1 tags after filtering in treatment: 21596644 INFO @ Fri, 10 Dec 2021 12:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:36:27: #1 finished! INFO @ Fri, 10 Dec 2021 12:36:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:36:29: #2 number of paired peaks: 122 WARNING @ Fri, 10 Dec 2021 12:36:29: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Fri, 10 Dec 2021 12:36:29: start model_add_line... INFO @ Fri, 10 Dec 2021 12:36:29: start X-correlation... INFO @ Fri, 10 Dec 2021 12:36:29: end of X-cor INFO @ Fri, 10 Dec 2021 12:36:29: #2 finished! INFO @ Fri, 10 Dec 2021 12:36:29: #2 predicted fragment length is 41 bps INFO @ Fri, 10 Dec 2021 12:36:29: #2 alternative fragment length(s) may be 3,12,41 bps INFO @ Fri, 10 Dec 2021 12:36:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.20_model.r WARNING @ Fri, 10 Dec 2021 12:36:29: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:36:29: #2 You may need to consider one of the other alternative d(s): 3,12,41 WARNING @ Fri, 10 Dec 2021 12:36:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:36:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:36:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:36:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:36:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:36:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.05_summits.bed INFO @ Fri, 10 Dec 2021 12:36:37: Done! pass1 - making usageList (400 chroms): 6 millis pass2 - checking and writing primary data (6918 records, 4 fields): 28 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:36:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:37:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:37:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:37:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.10_summits.bed INFO @ Fri, 10 Dec 2021 12:37:08: Done! pass1 - making usageList (234 chroms): 1 millis pass2 - checking and writing primary data (2262 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:37:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:37:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:37:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:37:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9717948/SRX9717948.20_summits.bed INFO @ Fri, 10 Dec 2021 12:37:33: Done! pass1 - making usageList (77 chroms): 27 millis pass2 - checking and writing primary data (166 records, 4 fields): 36 millis CompletedMACS2peakCalling