Job ID = 14167372 SRX = SRX8688939 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25495989 spots for SRR12174292/SRR12174292.sra Written 25495989 spots for SRR12174292/SRR12174292.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168027 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:57 25495989 reads; of these: 25495989 (100.00%) were unpaired; of these: 735207 (2.88%) aligned 0 times 16536450 (64.86%) aligned exactly 1 time 8224332 (32.26%) aligned >1 times 97.12% overall alignment rate Time searching: 00:12:57 Overall time: 00:12:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3492292 / 24760782 = 0.1410 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 12:24:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.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 12:24:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:24:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:24:18: 1000000 INFO @ Fri, 10 Dec 2021 12:24:26: 2000000 INFO @ Fri, 10 Dec 2021 12:24:34: 3000000 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 12:24:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.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 12:24:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:24:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:24:42: 4000000 INFO @ Fri, 10 Dec 2021 12:24:47: 1000000 INFO @ Fri, 10 Dec 2021 12:24:50: 5000000 INFO @ Fri, 10 Dec 2021 12:24:55: 2000000 INFO @ Fri, 10 Dec 2021 12:24:58: 6000000 INFO @ Fri, 10 Dec 2021 12:25:03: 3000000 INFO @ Fri, 10 Dec 2021 12:25:06: 7000000 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 12:25:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.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 12:25:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:25:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:25:11: 4000000 INFO @ Fri, 10 Dec 2021 12:25:14: 8000000 INFO @ Fri, 10 Dec 2021 12:25:19: 1000000 INFO @ Fri, 10 Dec 2021 12:25:20: 5000000 INFO @ Fri, 10 Dec 2021 12:25:23: 9000000 INFO @ Fri, 10 Dec 2021 12:25:27: 2000000 INFO @ Fri, 10 Dec 2021 12:25:28: 6000000 INFO @ Fri, 10 Dec 2021 12:25:31: 10000000 INFO @ Fri, 10 Dec 2021 12:25:35: 3000000 INFO @ Fri, 10 Dec 2021 12:25:36: 7000000 INFO @ Fri, 10 Dec 2021 12:25:39: 11000000 INFO @ Fri, 10 Dec 2021 12:25:44: 4000000 INFO @ Fri, 10 Dec 2021 12:25:45: 8000000 INFO @ Fri, 10 Dec 2021 12:25:48: 12000000 INFO @ Fri, 10 Dec 2021 12:25:53: 9000000 INFO @ Fri, 10 Dec 2021 12:25:53: 5000000 INFO @ Fri, 10 Dec 2021 12:25:56: 13000000 INFO @ Fri, 10 Dec 2021 12:26:01: 6000000 INFO @ Fri, 10 Dec 2021 12:26:01: 10000000 INFO @ Fri, 10 Dec 2021 12:26:04: 14000000 INFO @ Fri, 10 Dec 2021 12:26:10: 7000000 INFO @ Fri, 10 Dec 2021 12:26:10: 11000000 INFO @ Fri, 10 Dec 2021 12:26:14: 15000000 INFO @ Fri, 10 Dec 2021 12:26:18: 8000000 INFO @ Fri, 10 Dec 2021 12:26:19: 12000000 INFO @ Fri, 10 Dec 2021 12:26:24: 16000000 INFO @ Fri, 10 Dec 2021 12:26:27: 13000000 INFO @ Fri, 10 Dec 2021 12:26:28: 9000000 INFO @ Fri, 10 Dec 2021 12:26:34: 17000000 INFO @ Fri, 10 Dec 2021 12:26:36: 14000000 INFO @ Fri, 10 Dec 2021 12:26:37: 10000000 INFO @ Fri, 10 Dec 2021 12:26:43: 18000000 INFO @ Fri, 10 Dec 2021 12:26:45: 15000000 INFO @ Fri, 10 Dec 2021 12:26:47: 11000000 INFO @ Fri, 10 Dec 2021 12:26:53: 19000000 INFO @ Fri, 10 Dec 2021 12:26:55: 16000000 INFO @ Fri, 10 Dec 2021 12:26:57: 12000000 INFO @ Fri, 10 Dec 2021 12:27:03: 20000000 INFO @ Fri, 10 Dec 2021 12:27:05: 17000000 INFO @ Fri, 10 Dec 2021 12:27:06: 13000000 INFO @ Fri, 10 Dec 2021 12:27:12: 21000000 INFO @ Fri, 10 Dec 2021 12:27:15: 18000000 INFO @ Fri, 10 Dec 2021 12:27:15: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:27:15: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:27:15: #1 total tags in treatment: 21268490 INFO @ Fri, 10 Dec 2021 12:27:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:27:15: #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 12:27:16: #1 tags after filtering in treatment: 21268490 INFO @ Fri, 10 Dec 2021 12:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:27:16: #1 finished! INFO @ Fri, 10 Dec 2021 12:27:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:27:17: #2 number of paired peaks: 164 WARNING @ Fri, 10 Dec 2021 12:27:17: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 10 Dec 2021 12:27:17: start model_add_line... INFO @ Fri, 10 Dec 2021 12:27:17: start X-correlation... INFO @ Fri, 10 Dec 2021 12:27:17: end of X-cor INFO @ Fri, 10 Dec 2021 12:27:17: #2 finished! INFO @ Fri, 10 Dec 2021 12:27:17: #2 predicted fragment length is 40 bps INFO @ Fri, 10 Dec 2021 12:27:17: #2 alternative fragment length(s) may be 40 bps INFO @ Fri, 10 Dec 2021 12:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.05_model.r WARNING @ Fri, 10 Dec 2021 12:27:17: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:27:17: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Fri, 10 Dec 2021 12:27:17: #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 12:27:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:27:18: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:27:26: 19000000 INFO @ Fri, 10 Dec 2021 12:27:29: 15000000 INFO @ Fri, 10 Dec 2021 12:27:35: 20000000 INFO @ Fri, 10 Dec 2021 12:27:40: 16000000 INFO @ Fri, 10 Dec 2021 12:27:45: 21000000 INFO @ Fri, 10 Dec 2021 12:27:49: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:27:49: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:27:49: #1 total tags in treatment: 21268490 INFO @ Fri, 10 Dec 2021 12:27:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:27:49: #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 12:27:49: #1 tags after filtering in treatment: 21268490 INFO @ Fri, 10 Dec 2021 12:27:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:27:49: #1 finished! INFO @ Fri, 10 Dec 2021 12:27:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:27:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:27:50: 17000000 INFO @ Fri, 10 Dec 2021 12:27:50: #2 number of paired peaks: 164 WARNING @ Fri, 10 Dec 2021 12:27:50: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 10 Dec 2021 12:27:50: start model_add_line... INFO @ Fri, 10 Dec 2021 12:27:50: start X-correlation... INFO @ Fri, 10 Dec 2021 12:27:50: end of X-cor INFO @ Fri, 10 Dec 2021 12:27:50: #2 finished! INFO @ Fri, 10 Dec 2021 12:27:50: #2 predicted fragment length is 40 bps INFO @ Fri, 10 Dec 2021 12:27:50: #2 alternative fragment length(s) may be 40 bps INFO @ Fri, 10 Dec 2021 12:27:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.10_model.r WARNING @ Fri, 10 Dec 2021 12:27:50: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:27:50: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Fri, 10 Dec 2021 12:27:50: #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 12:27:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:27:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:27:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:28:01: 18000000 INFO @ Fri, 10 Dec 2021 12:28:13: 19000000 INFO @ Fri, 10 Dec 2021 12:28:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:28:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:28:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.05_summits.bed INFO @ Fri, 10 Dec 2021 12:28:15: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2143 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:28:24: 20000000 INFO @ Fri, 10 Dec 2021 12:28:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:28:35: 21000000 INFO @ Fri, 10 Dec 2021 12:28:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:28:37: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:28:37: #1 total tags in treatment: 21268490 INFO @ Fri, 10 Dec 2021 12:28:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:28:37: #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 12:28:38: #1 tags after filtering in treatment: 21268490 INFO @ Fri, 10 Dec 2021 12:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:28:38: #1 finished! INFO @ Fri, 10 Dec 2021 12:28:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:28:39: #2 number of paired peaks: 164 WARNING @ Fri, 10 Dec 2021 12:28:39: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 10 Dec 2021 12:28:39: start model_add_line... INFO @ Fri, 10 Dec 2021 12:28:39: start X-correlation... INFO @ Fri, 10 Dec 2021 12:28:39: end of X-cor INFO @ Fri, 10 Dec 2021 12:28:39: #2 finished! INFO @ Fri, 10 Dec 2021 12:28:39: #2 predicted fragment length is 40 bps INFO @ Fri, 10 Dec 2021 12:28:39: #2 alternative fragment length(s) may be 40 bps INFO @ Fri, 10 Dec 2021 12:28:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.20_model.r WARNING @ Fri, 10 Dec 2021 12:28:39: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:28:39: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Fri, 10 Dec 2021 12:28:39: #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 12:28:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:28:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.10_summits.bed INFO @ Fri, 10 Dec 2021 12:28:48: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1553 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:29:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688939/SRX8688939.20_summits.bed INFO @ Fri, 10 Dec 2021 12:29:35: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1165 records, 4 fields): 4 millis CompletedMACS2peakCalling