Job ID = 14167649 SRX = SRX4712957 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: 00:08:20 30167676 reads; of these: 30167676 (100.00%) were unpaired; of these: 870489 (2.89%) aligned 0 times 22011841 (72.96%) aligned exactly 1 time 7285346 (24.15%) aligned >1 times 97.11% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 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] 4533668 / 29297187 = 0.1547 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 13:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.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 13:12:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:12:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:12:27: 1000000 INFO @ Fri, 10 Dec 2021 13:12:33: 2000000 INFO @ Fri, 10 Dec 2021 13:12:39: 3000000 INFO @ Fri, 10 Dec 2021 13:12:44: 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 13:12:50: 5000000 INFO @ Fri, 10 Dec 2021 13:12:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.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 13:12:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:12:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:12:57: 6000000 INFO @ Fri, 10 Dec 2021 13:12:58: 1000000 INFO @ Fri, 10 Dec 2021 13:13:03: 7000000 INFO @ Fri, 10 Dec 2021 13:13:06: 2000000 INFO @ Fri, 10 Dec 2021 13:13:10: 8000000 INFO @ Fri, 10 Dec 2021 13:13:13: 3000000 INFO @ Fri, 10 Dec 2021 13:13:16: 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 @ Fri, 10 Dec 2021 13:13:20: 4000000 INFO @ Fri, 10 Dec 2021 13:13:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.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 13:13:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:13:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:13:23: 10000000 INFO @ Fri, 10 Dec 2021 13:13:28: 5000000 INFO @ Fri, 10 Dec 2021 13:13:28: 1000000 INFO @ Fri, 10 Dec 2021 13:13:30: 11000000 INFO @ Fri, 10 Dec 2021 13:13:35: 2000000 INFO @ Fri, 10 Dec 2021 13:13:35: 6000000 INFO @ Fri, 10 Dec 2021 13:13:37: 12000000 INFO @ Fri, 10 Dec 2021 13:13:42: 3000000 INFO @ Fri, 10 Dec 2021 13:13:42: 7000000 INFO @ Fri, 10 Dec 2021 13:13:44: 13000000 INFO @ Fri, 10 Dec 2021 13:13:49: 4000000 INFO @ Fri, 10 Dec 2021 13:13:50: 8000000 INFO @ Fri, 10 Dec 2021 13:13:51: 14000000 INFO @ Fri, 10 Dec 2021 13:13:56: 5000000 INFO @ Fri, 10 Dec 2021 13:13:57: 9000000 INFO @ Fri, 10 Dec 2021 13:13:58: 15000000 INFO @ Fri, 10 Dec 2021 13:14:03: 6000000 INFO @ Fri, 10 Dec 2021 13:14:04: 10000000 INFO @ Fri, 10 Dec 2021 13:14:05: 16000000 INFO @ Fri, 10 Dec 2021 13:14:10: 7000000 INFO @ Fri, 10 Dec 2021 13:14:11: 11000000 INFO @ Fri, 10 Dec 2021 13:14:12: 17000000 INFO @ Fri, 10 Dec 2021 13:14:17: 8000000 INFO @ Fri, 10 Dec 2021 13:14:19: 12000000 INFO @ Fri, 10 Dec 2021 13:14:19: 18000000 INFO @ Fri, 10 Dec 2021 13:14:24: 9000000 INFO @ Fri, 10 Dec 2021 13:14:26: 19000000 INFO @ Fri, 10 Dec 2021 13:14:26: 13000000 INFO @ Fri, 10 Dec 2021 13:14:30: 10000000 INFO @ Fri, 10 Dec 2021 13:14:33: 20000000 INFO @ Fri, 10 Dec 2021 13:14:33: 14000000 INFO @ Fri, 10 Dec 2021 13:14:37: 11000000 INFO @ Fri, 10 Dec 2021 13:14:40: 21000000 INFO @ Fri, 10 Dec 2021 13:14:41: 15000000 INFO @ Fri, 10 Dec 2021 13:14:44: 12000000 INFO @ Fri, 10 Dec 2021 13:14:47: 22000000 INFO @ Fri, 10 Dec 2021 13:14:48: 16000000 INFO @ Fri, 10 Dec 2021 13:14:51: 13000000 INFO @ Fri, 10 Dec 2021 13:14:53: 23000000 INFO @ Fri, 10 Dec 2021 13:14:56: 17000000 INFO @ Fri, 10 Dec 2021 13:14:58: 14000000 INFO @ Fri, 10 Dec 2021 13:15:00: 24000000 INFO @ Fri, 10 Dec 2021 13:15:03: 18000000 INFO @ Fri, 10 Dec 2021 13:15:05: 15000000 INFO @ Fri, 10 Dec 2021 13:15:06: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:15:06: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:15:06: #1 total tags in treatment: 24763519 INFO @ Fri, 10 Dec 2021 13:15:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:15:06: #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 13:15:07: #1 tags after filtering in treatment: 24763514 INFO @ Fri, 10 Dec 2021 13:15:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:15:07: #1 finished! INFO @ Fri, 10 Dec 2021 13:15:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:15:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:15:08: #2 number of paired peaks: 193 WARNING @ Fri, 10 Dec 2021 13:15:08: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Fri, 10 Dec 2021 13:15:08: start model_add_line... INFO @ Fri, 10 Dec 2021 13:15:09: start X-correlation... INFO @ Fri, 10 Dec 2021 13:15:09: end of X-cor INFO @ Fri, 10 Dec 2021 13:15:09: #2 finished! INFO @ Fri, 10 Dec 2021 13:15:09: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 13:15:09: #2 alternative fragment length(s) may be 3,48,592 bps INFO @ Fri, 10 Dec 2021 13:15:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.05_model.r WARNING @ Fri, 10 Dec 2021 13:15:09: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:15:09: #2 You may need to consider one of the other alternative d(s): 3,48,592 WARNING @ Fri, 10 Dec 2021 13:15:09: #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 13:15:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:15:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:15:11: 19000000 INFO @ Fri, 10 Dec 2021 13:15:12: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:15:18: 20000000 INFO @ Fri, 10 Dec 2021 13:15:18: 17000000 INFO @ Fri, 10 Dec 2021 13:15:25: 18000000 INFO @ Fri, 10 Dec 2021 13:15:26: 21000000 INFO @ Fri, 10 Dec 2021 13:15:32: 19000000 INFO @ Fri, 10 Dec 2021 13:15:33: 22000000 INFO @ Fri, 10 Dec 2021 13:15:39: 20000000 INFO @ Fri, 10 Dec 2021 13:15:40: 23000000 INFO @ Fri, 10 Dec 2021 13:15:46: 21000000 INFO @ Fri, 10 Dec 2021 13:15:47: 24000000 INFO @ Fri, 10 Dec 2021 13:15:53: 22000000 INFO @ Fri, 10 Dec 2021 13:15:53: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:15:53: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:15:53: #1 total tags in treatment: 24763519 INFO @ Fri, 10 Dec 2021 13:15:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:15:53: #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 13:15:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:15:54: #1 tags after filtering in treatment: 24763514 INFO @ Fri, 10 Dec 2021 13:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:15:54: #1 finished! INFO @ Fri, 10 Dec 2021 13:15:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:15:55: #2 number of paired peaks: 193 WARNING @ Fri, 10 Dec 2021 13:15:55: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Fri, 10 Dec 2021 13:15:55: start model_add_line... INFO @ Fri, 10 Dec 2021 13:15:56: start X-correlation... INFO @ Fri, 10 Dec 2021 13:15:56: end of X-cor INFO @ Fri, 10 Dec 2021 13:15:56: #2 finished! INFO @ Fri, 10 Dec 2021 13:15:56: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 13:15:56: #2 alternative fragment length(s) may be 3,48,592 bps INFO @ Fri, 10 Dec 2021 13:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.10_model.r WARNING @ Fri, 10 Dec 2021 13:15:56: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:15:56: #2 You may need to consider one of the other alternative d(s): 3,48,592 WARNING @ Fri, 10 Dec 2021 13:15:56: #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 13:15:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:15:59: 23000000 INFO @ Fri, 10 Dec 2021 13:16:05: 24000000 INFO @ Fri, 10 Dec 2021 13:16:10: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:16:10: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:16:10: #1 total tags in treatment: 24763519 INFO @ Fri, 10 Dec 2021 13:16:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:16:10: #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 13:16:10: #1 tags after filtering in treatment: 24763514 INFO @ Fri, 10 Dec 2021 13:16:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:16:10: #1 finished! INFO @ Fri, 10 Dec 2021 13:16:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:16:10: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:16:12: #2 number of paired peaks: 193 WARNING @ Fri, 10 Dec 2021 13:16:12: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Fri, 10 Dec 2021 13:16:12: start model_add_line... INFO @ Fri, 10 Dec 2021 13:16:12: start X-correlation... INFO @ Fri, 10 Dec 2021 13:16:12: end of X-cor INFO @ Fri, 10 Dec 2021 13:16:12: #2 finished! INFO @ Fri, 10 Dec 2021 13:16:12: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 13:16:12: #2 alternative fragment length(s) may be 3,48,592 bps INFO @ Fri, 10 Dec 2021 13:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.20_model.r WARNING @ Fri, 10 Dec 2021 13:16:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:16:12: #2 You may need to consider one of the other alternative d(s): 3,48,592 WARNING @ Fri, 10 Dec 2021 13:16:12: #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 13:16:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:16:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:16:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:16:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.05_summits.bed INFO @ Fri, 10 Dec 2021 13:16:17: Done! pass1 - making usageList (497 chroms): 1 millis pass2 - checking and writing primary data (4430 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:16:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:16:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.10_summits.bed INFO @ Fri, 10 Dec 2021 13:17:02: Done! pass1 - making usageList (388 chroms): 2 millis pass2 - checking and writing primary data (1562 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712957/SRX4712957.20_summits.bed INFO @ Fri, 10 Dec 2021 13:17:21: Done! pass1 - making usageList (235 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 11 millis CompletedMACS2peakCalling