Job ID = 14168015 SRX = SRX8688936 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:35 21602640 reads; of these: 21602640 (100.00%) were unpaired; of these: 821303 (3.80%) aligned 0 times 14138920 (65.45%) aligned exactly 1 time 6642417 (30.75%) aligned >1 times 96.20% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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] 3238795 / 20781337 = 0.1559 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 14:32:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.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 14:32:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:32:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:32:39: 1000000 INFO @ Fri, 10 Dec 2021 14:32:45: 2000000 INFO @ Fri, 10 Dec 2021 14:32:50: 3000000 INFO @ Fri, 10 Dec 2021 14:32:56: 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 @ Fri, 10 Dec 2021 14:33:02: 5000000 INFO @ Fri, 10 Dec 2021 14:33:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.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 14:33:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:33:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:33:08: 6000000 INFO @ Fri, 10 Dec 2021 14:33:09: 1000000 INFO @ Fri, 10 Dec 2021 14:33:14: 7000000 INFO @ Fri, 10 Dec 2021 14:33:16: 2000000 INFO @ Fri, 10 Dec 2021 14:33:20: 8000000 INFO @ Fri, 10 Dec 2021 14:33:22: 3000000 INFO @ Fri, 10 Dec 2021 14:33:27: 9000000 INFO @ Fri, 10 Dec 2021 14:33:28: 4000000 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 14:33:33: 10000000 INFO @ Fri, 10 Dec 2021 14:33:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.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 14:33:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:33:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:33:35: 5000000 INFO @ Fri, 10 Dec 2021 14:33:39: 11000000 INFO @ Fri, 10 Dec 2021 14:33:40: 1000000 INFO @ Fri, 10 Dec 2021 14:33:41: 6000000 INFO @ Fri, 10 Dec 2021 14:33:46: 12000000 INFO @ Fri, 10 Dec 2021 14:33:46: 2000000 INFO @ Fri, 10 Dec 2021 14:33:48: 7000000 INFO @ Fri, 10 Dec 2021 14:33:52: 13000000 INFO @ Fri, 10 Dec 2021 14:33:52: 3000000 INFO @ Fri, 10 Dec 2021 14:33:54: 8000000 INFO @ Fri, 10 Dec 2021 14:33:58: 14000000 INFO @ Fri, 10 Dec 2021 14:33:59: 4000000 INFO @ Fri, 10 Dec 2021 14:34:00: 9000000 INFO @ Fri, 10 Dec 2021 14:34:05: 15000000 INFO @ Fri, 10 Dec 2021 14:34:05: 5000000 INFO @ Fri, 10 Dec 2021 14:34:07: 10000000 INFO @ Fri, 10 Dec 2021 14:34:11: 16000000 INFO @ Fri, 10 Dec 2021 14:34:12: 6000000 INFO @ Fri, 10 Dec 2021 14:34:13: 11000000 INFO @ Fri, 10 Dec 2021 14:34:18: 17000000 INFO @ Fri, 10 Dec 2021 14:34:18: 7000000 INFO @ Fri, 10 Dec 2021 14:34:20: 12000000 INFO @ Fri, 10 Dec 2021 14:34:21: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:34:21: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:34:21: #1 total tags in treatment: 17542542 INFO @ Fri, 10 Dec 2021 14:34:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:34:21: #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 14:34:22: #1 tags after filtering in treatment: 17542541 INFO @ Fri, 10 Dec 2021 14:34:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:34:22: #1 finished! INFO @ Fri, 10 Dec 2021 14:34:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:34:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:34:23: #2 number of paired peaks: 348 WARNING @ Fri, 10 Dec 2021 14:34:23: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 10 Dec 2021 14:34:23: start model_add_line... INFO @ Fri, 10 Dec 2021 14:34:23: start X-correlation... INFO @ Fri, 10 Dec 2021 14:34:23: end of X-cor INFO @ Fri, 10 Dec 2021 14:34:23: #2 finished! INFO @ Fri, 10 Dec 2021 14:34:23: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 14:34:23: #2 alternative fragment length(s) may be 4,45 bps INFO @ Fri, 10 Dec 2021 14:34:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.05_model.r WARNING @ Fri, 10 Dec 2021 14:34:23: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:34:23: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Fri, 10 Dec 2021 14:34:23: #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 14:34:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:34:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:34:24: 8000000 INFO @ Fri, 10 Dec 2021 14:34:26: 13000000 INFO @ Fri, 10 Dec 2021 14:34:30: 9000000 INFO @ Fri, 10 Dec 2021 14:34:32: 14000000 INFO @ Fri, 10 Dec 2021 14:34:37: 10000000 INFO @ Fri, 10 Dec 2021 14:34:39: 15000000 INFO @ Fri, 10 Dec 2021 14:34:43: 11000000 INFO @ Fri, 10 Dec 2021 14:34:45: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:34:49: 12000000 INFO @ Fri, 10 Dec 2021 14:34:52: 17000000 INFO @ Fri, 10 Dec 2021 14:34:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:34:55: 13000000 INFO @ Fri, 10 Dec 2021 14:34:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:34:56: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:34:56: #1 total tags in treatment: 17542542 INFO @ Fri, 10 Dec 2021 14:34:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:34:56: #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 14:34:56: #1 tags after filtering in treatment: 17542541 INFO @ Fri, 10 Dec 2021 14:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:34:56: #1 finished! INFO @ Fri, 10 Dec 2021 14:34:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:34:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:34:57: #2 number of paired peaks: 348 WARNING @ Fri, 10 Dec 2021 14:34:57: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 10 Dec 2021 14:34:57: start model_add_line... INFO @ Fri, 10 Dec 2021 14:34:57: start X-correlation... INFO @ Fri, 10 Dec 2021 14:34:57: end of X-cor INFO @ Fri, 10 Dec 2021 14:34:57: #2 finished! INFO @ Fri, 10 Dec 2021 14:34:57: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 14:34:57: #2 alternative fragment length(s) may be 4,45 bps INFO @ Fri, 10 Dec 2021 14:34:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.10_model.r WARNING @ Fri, 10 Dec 2021 14:34:57: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:34:57: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Fri, 10 Dec 2021 14:34:57: #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 14:34:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:34:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:35:01: 14000000 INFO @ Fri, 10 Dec 2021 14:35:08: 15000000 INFO @ Fri, 10 Dec 2021 14:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.05_summits.bed INFO @ Fri, 10 Dec 2021 14:35:08: Done! pass1 - making usageList (727 chroms): 1 millis pass2 - checking and writing primary data (3101 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:35:14: 16000000 INFO @ Fri, 10 Dec 2021 14:35:19: 17000000 INFO @ Fri, 10 Dec 2021 14:35:23: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:35:23: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:35:23: #1 total tags in treatment: 17542542 INFO @ Fri, 10 Dec 2021 14:35:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:35:23: #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 14:35:23: #1 tags after filtering in treatment: 17542541 INFO @ Fri, 10 Dec 2021 14:35:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:35:23: #1 finished! INFO @ Fri, 10 Dec 2021 14:35:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:35:24: #2 number of paired peaks: 348 WARNING @ Fri, 10 Dec 2021 14:35:24: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 10 Dec 2021 14:35:24: start model_add_line... INFO @ Fri, 10 Dec 2021 14:35:24: start X-correlation... INFO @ Fri, 10 Dec 2021 14:35:24: end of X-cor INFO @ Fri, 10 Dec 2021 14:35:24: #2 finished! INFO @ Fri, 10 Dec 2021 14:35:24: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 14:35:24: #2 alternative fragment length(s) may be 4,45 bps INFO @ Fri, 10 Dec 2021 14:35:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.20_model.r WARNING @ Fri, 10 Dec 2021 14:35:24: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:35:24: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Fri, 10 Dec 2021 14:35:24: #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 14:35:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:35:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:35:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:35:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:35:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:35:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.10_summits.bed INFO @ Fri, 10 Dec 2021 14:35:42: Done! pass1 - making usageList (472 chroms): 1 millis pass2 - checking and writing primary data (1505 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:35:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:36:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:36:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:36:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688936/SRX8688936.20_summits.bed INFO @ Fri, 10 Dec 2021 14:36:09: Done! pass1 - making usageList (218 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 8 millis CompletedMACS2peakCalling