Job ID = 14167413 SRX = SRX8574271 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: 00:07:49 30783256 reads; of these: 30783256 (100.00%) were unpaired; of these: 3364660 (10.93%) aligned 0 times 18936526 (61.52%) aligned exactly 1 time 8482070 (27.55%) aligned >1 times 89.07% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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] 6176298 / 27418596 = 0.2253 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 12:26:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.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 12:26:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:26:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:26:55: 1000000 INFO @ Fri, 10 Dec 2021 12:27:00: 2000000 INFO @ Fri, 10 Dec 2021 12:27:06: 3000000 INFO @ Fri, 10 Dec 2021 12:27:11: 4000000 INFO @ Fri, 10 Dec 2021 12:27:17: 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 12:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.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 12:27:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:27:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:27:22: 6000000 INFO @ Fri, 10 Dec 2021 12:27:25: 1000000 INFO @ Fri, 10 Dec 2021 12:27:28: 7000000 INFO @ Fri, 10 Dec 2021 12:27:31: 2000000 INFO @ Fri, 10 Dec 2021 12:27:34: 8000000 INFO @ Fri, 10 Dec 2021 12:27:36: 3000000 INFO @ Fri, 10 Dec 2021 12:27:39: 9000000 INFO @ Fri, 10 Dec 2021 12:27:42: 4000000 INFO @ Fri, 10 Dec 2021 12:27:45: 10000000 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 12:27:48: 5000000 INFO @ Fri, 10 Dec 2021 12:27:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.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 12:27:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:27:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:27:51: 11000000 INFO @ Fri, 10 Dec 2021 12:27:54: 6000000 INFO @ Fri, 10 Dec 2021 12:27:55: 1000000 INFO @ Fri, 10 Dec 2021 12:27:56: 12000000 INFO @ Fri, 10 Dec 2021 12:28:00: 7000000 INFO @ Fri, 10 Dec 2021 12:28:01: 2000000 INFO @ Fri, 10 Dec 2021 12:28:02: 13000000 INFO @ Fri, 10 Dec 2021 12:28:06: 8000000 INFO @ Fri, 10 Dec 2021 12:28:07: 3000000 INFO @ Fri, 10 Dec 2021 12:28:08: 14000000 INFO @ Fri, 10 Dec 2021 12:28:11: 9000000 INFO @ Fri, 10 Dec 2021 12:28:13: 4000000 INFO @ Fri, 10 Dec 2021 12:28:13: 15000000 INFO @ Fri, 10 Dec 2021 12:28:17: 10000000 INFO @ Fri, 10 Dec 2021 12:28:19: 5000000 INFO @ Fri, 10 Dec 2021 12:28:19: 16000000 INFO @ Fri, 10 Dec 2021 12:28:23: 11000000 INFO @ Fri, 10 Dec 2021 12:28:25: 6000000 INFO @ Fri, 10 Dec 2021 12:28:25: 17000000 INFO @ Fri, 10 Dec 2021 12:28:29: 12000000 INFO @ Fri, 10 Dec 2021 12:28:31: 7000000 INFO @ Fri, 10 Dec 2021 12:28:31: 18000000 INFO @ Fri, 10 Dec 2021 12:28:35: 13000000 INFO @ Fri, 10 Dec 2021 12:28:37: 8000000 INFO @ Fri, 10 Dec 2021 12:28:37: 19000000 INFO @ Fri, 10 Dec 2021 12:28:41: 14000000 INFO @ Fri, 10 Dec 2021 12:28:42: 9000000 INFO @ Fri, 10 Dec 2021 12:28:43: 20000000 INFO @ Fri, 10 Dec 2021 12:28:47: 15000000 INFO @ Fri, 10 Dec 2021 12:28:48: 10000000 INFO @ Fri, 10 Dec 2021 12:28:49: 21000000 INFO @ Fri, 10 Dec 2021 12:28:50: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:28:50: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:28:50: #1 total tags in treatment: 21242298 INFO @ Fri, 10 Dec 2021 12:28:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:28:50: #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 12:28:51: #1 tags after filtering in treatment: 21242298 INFO @ Fri, 10 Dec 2021 12:28:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:28:51: #1 finished! INFO @ Fri, 10 Dec 2021 12:28:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:28:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:28:52: #2 number of paired peaks: 570 WARNING @ Fri, 10 Dec 2021 12:28:52: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Fri, 10 Dec 2021 12:28:52: start model_add_line... INFO @ Fri, 10 Dec 2021 12:28:52: start X-correlation... INFO @ Fri, 10 Dec 2021 12:28:52: end of X-cor INFO @ Fri, 10 Dec 2021 12:28:52: #2 finished! INFO @ Fri, 10 Dec 2021 12:28:52: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:28:52: #2 alternative fragment length(s) may be 2,45 bps INFO @ Fri, 10 Dec 2021 12:28:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.05_model.r WARNING @ Fri, 10 Dec 2021 12:28:52: #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 12:28:52: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Fri, 10 Dec 2021 12:28:52: #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 12:28:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:28:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:28:53: 16000000 INFO @ Fri, 10 Dec 2021 12:28:54: 11000000 INFO @ Fri, 10 Dec 2021 12:28:59: 17000000 INFO @ Fri, 10 Dec 2021 12:29:00: 12000000 INFO @ Fri, 10 Dec 2021 12:29:05: 18000000 INFO @ Fri, 10 Dec 2021 12:29:06: 13000000 INFO @ Fri, 10 Dec 2021 12:29:11: 19000000 INFO @ Fri, 10 Dec 2021 12:29:12: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:29:17: 20000000 INFO @ Fri, 10 Dec 2021 12:29:17: 15000000 INFO @ Fri, 10 Dec 2021 12:29:23: 21000000 INFO @ Fri, 10 Dec 2021 12:29:23: 16000000 INFO @ Fri, 10 Dec 2021 12:29:24: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:29:24: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:29:24: #1 total tags in treatment: 21242298 INFO @ Fri, 10 Dec 2021 12:29:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:29:24: #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 12:29:25: #1 tags after filtering in treatment: 21242298 INFO @ Fri, 10 Dec 2021 12:29:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:29:25: #1 finished! INFO @ Fri, 10 Dec 2021 12:29:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:29:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:29:26: #2 number of paired peaks: 570 WARNING @ Fri, 10 Dec 2021 12:29:26: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Fri, 10 Dec 2021 12:29:26: start model_add_line... INFO @ Fri, 10 Dec 2021 12:29:26: start X-correlation... INFO @ Fri, 10 Dec 2021 12:29:26: end of X-cor INFO @ Fri, 10 Dec 2021 12:29:26: #2 finished! INFO @ Fri, 10 Dec 2021 12:29:26: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:29:26: #2 alternative fragment length(s) may be 2,45 bps INFO @ Fri, 10 Dec 2021 12:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.10_model.r WARNING @ Fri, 10 Dec 2021 12:29:26: #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 12:29:26: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Fri, 10 Dec 2021 12:29:26: #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 12:29:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:29:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:29:29: 17000000 INFO @ Fri, 10 Dec 2021 12:29:35: 18000000 INFO @ Fri, 10 Dec 2021 12:29:40: 19000000 INFO @ Fri, 10 Dec 2021 12:29:46: 20000000 INFO @ Fri, 10 Dec 2021 12:29:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:29:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:29:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.05_summits.bed INFO @ Fri, 10 Dec 2021 12:29:46: Done! pass1 - making usageList (806 chroms): 1 millis pass2 - checking and writing primary data (3325 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:29:52: 21000000 INFO @ Fri, 10 Dec 2021 12:29:53: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:29:53: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:29:53: #1 total tags in treatment: 21242298 INFO @ Fri, 10 Dec 2021 12:29:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:29:53: #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 12:29:54: #1 tags after filtering in treatment: 21242298 INFO @ Fri, 10 Dec 2021 12:29:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:29:54: #1 finished! INFO @ Fri, 10 Dec 2021 12:29:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:29:55: #2 number of paired peaks: 570 WARNING @ Fri, 10 Dec 2021 12:29:55: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Fri, 10 Dec 2021 12:29:55: start model_add_line... INFO @ Fri, 10 Dec 2021 12:29:55: start X-correlation... INFO @ Fri, 10 Dec 2021 12:29:55: end of X-cor INFO @ Fri, 10 Dec 2021 12:29:55: #2 finished! INFO @ Fri, 10 Dec 2021 12:29:55: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:29:55: #2 alternative fragment length(s) may be 2,45 bps INFO @ Fri, 10 Dec 2021 12:29:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.20_model.r WARNING @ Fri, 10 Dec 2021 12:29:55: #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 12:29:55: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Fri, 10 Dec 2021 12:29:55: #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 12:29:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:29:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:30:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.10_summits.bed INFO @ Fri, 10 Dec 2021 12:30:21: Done! pass1 - making usageList (673 chroms): 1 millis pass2 - checking and writing primary data (2545 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:30:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:30:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:30:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:30:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574271/SRX8574271.20_summits.bed INFO @ Fri, 10 Dec 2021 12:30:49: Done! pass1 - making usageList (468 chroms): 1 millis pass2 - checking and writing primary data (1300 records, 4 fields): 21 millis CompletedMACS2peakCalling