Job ID = 14167369 SRX = SRX8688937 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23229247 spots for SRR12174289/SRR12174289.sra Written 23229247 spots for SRR12174289/SRR12174289.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168012 ("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: 00:09:20 23229247 reads; of these: 23229247 (100.00%) were unpaired; of these: 653877 (2.81%) aligned 0 times 14991352 (64.54%) aligned exactly 1 time 7584018 (32.65%) aligned >1 times 97.19% overall alignment rate Time searching: 00:09:20 Overall time: 00:09:20 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] 3108693 / 22575370 = 0.1377 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 12:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.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 12:17:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:17:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:17:21: 1000000 INFO @ Fri, 10 Dec 2021 12:17:27: 2000000 INFO @ Fri, 10 Dec 2021 12:17:33: 3000000 INFO @ Fri, 10 Dec 2021 12:17:38: 4000000 INFO @ Fri, 10 Dec 2021 12:17:44: 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 12:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.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 12:17:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:17:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:17:50: 6000000 INFO @ Fri, 10 Dec 2021 12:17:52: 1000000 INFO @ Fri, 10 Dec 2021 12:17:55: 7000000 INFO @ Fri, 10 Dec 2021 12:17:58: 2000000 INFO @ Fri, 10 Dec 2021 12:18:01: 8000000 INFO @ Fri, 10 Dec 2021 12:18:04: 3000000 INFO @ Fri, 10 Dec 2021 12:18:07: 9000000 INFO @ Fri, 10 Dec 2021 12:18:10: 4000000 INFO @ Fri, 10 Dec 2021 12:18:13: 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 12:18:16: 5000000 INFO @ Fri, 10 Dec 2021 12:18:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.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 12:18:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:18:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:18:19: 11000000 INFO @ Fri, 10 Dec 2021 12:18:21: 1000000 INFO @ Fri, 10 Dec 2021 12:18:21: 6000000 INFO @ Fri, 10 Dec 2021 12:18:25: 12000000 INFO @ Fri, 10 Dec 2021 12:18:26: 2000000 INFO @ Fri, 10 Dec 2021 12:18:27: 7000000 INFO @ Fri, 10 Dec 2021 12:18:31: 13000000 INFO @ Fri, 10 Dec 2021 12:18:31: 3000000 INFO @ Fri, 10 Dec 2021 12:18:33: 8000000 INFO @ Fri, 10 Dec 2021 12:18:37: 4000000 INFO @ Fri, 10 Dec 2021 12:18:37: 14000000 INFO @ Fri, 10 Dec 2021 12:18:39: 9000000 INFO @ Fri, 10 Dec 2021 12:18:42: 5000000 INFO @ Fri, 10 Dec 2021 12:18:43: 15000000 INFO @ Fri, 10 Dec 2021 12:18:44: 10000000 INFO @ Fri, 10 Dec 2021 12:18:47: 6000000 INFO @ Fri, 10 Dec 2021 12:18:49: 16000000 INFO @ Fri, 10 Dec 2021 12:18:50: 11000000 INFO @ Fri, 10 Dec 2021 12:18:53: 7000000 INFO @ Fri, 10 Dec 2021 12:18:56: 17000000 INFO @ Fri, 10 Dec 2021 12:18:56: 12000000 INFO @ Fri, 10 Dec 2021 12:18:58: 8000000 INFO @ Fri, 10 Dec 2021 12:19:02: 18000000 INFO @ Fri, 10 Dec 2021 12:19:02: 13000000 INFO @ Fri, 10 Dec 2021 12:19:03: 9000000 INFO @ Fri, 10 Dec 2021 12:19:08: 14000000 INFO @ Fri, 10 Dec 2021 12:19:08: 19000000 INFO @ Fri, 10 Dec 2021 12:19:08: 10000000 INFO @ Fri, 10 Dec 2021 12:19:11: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:19:11: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:19:11: #1 total tags in treatment: 19466677 INFO @ Fri, 10 Dec 2021 12:19:11: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:19:11: #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 12:19:11: #1 tags after filtering in treatment: 19466677 INFO @ Fri, 10 Dec 2021 12:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:19:11: #1 finished! INFO @ Fri, 10 Dec 2021 12:19:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:19:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:19:12: #2 number of paired peaks: 209 WARNING @ Fri, 10 Dec 2021 12:19:12: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 10 Dec 2021 12:19:12: start model_add_line... INFO @ Fri, 10 Dec 2021 12:19:12: start X-correlation... INFO @ Fri, 10 Dec 2021 12:19:12: end of X-cor INFO @ Fri, 10 Dec 2021 12:19:12: #2 finished! INFO @ Fri, 10 Dec 2021 12:19:12: #2 predicted fragment length is 39 bps INFO @ Fri, 10 Dec 2021 12:19:12: #2 alternative fragment length(s) may be 39 bps INFO @ Fri, 10 Dec 2021 12:19:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.05_model.r WARNING @ Fri, 10 Dec 2021 12:19:12: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:19:12: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Fri, 10 Dec 2021 12:19:12: #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 12:19:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:19:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:19:13: 15000000 INFO @ Fri, 10 Dec 2021 12:19:13: 11000000 INFO @ Fri, 10 Dec 2021 12:19:19: 12000000 INFO @ Fri, 10 Dec 2021 12:19:19: 16000000 INFO @ Fri, 10 Dec 2021 12:19:24: 13000000 INFO @ Fri, 10 Dec 2021 12:19:25: 17000000 INFO @ Fri, 10 Dec 2021 12:19:29: 14000000 INFO @ Fri, 10 Dec 2021 12:19:31: 18000000 INFO @ Fri, 10 Dec 2021 12:19:34: 15000000 INFO @ Fri, 10 Dec 2021 12:19:36: 19000000 INFO @ Fri, 10 Dec 2021 12:19:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:19:39: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:19:39: #1 total tags in treatment: 19466677 INFO @ Fri, 10 Dec 2021 12:19:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:19:39: #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 12:19:39: 16000000 INFO @ Fri, 10 Dec 2021 12:19:40: #1 tags after filtering in treatment: 19466677 INFO @ Fri, 10 Dec 2021 12:19:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:19:40: #1 finished! INFO @ Fri, 10 Dec 2021 12:19:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:19:40: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:19:41: #2 number of paired peaks: 209 WARNING @ Fri, 10 Dec 2021 12:19:41: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 10 Dec 2021 12:19:41: start model_add_line... INFO @ Fri, 10 Dec 2021 12:19:41: start X-correlation... INFO @ Fri, 10 Dec 2021 12:19:41: end of X-cor INFO @ Fri, 10 Dec 2021 12:19:41: #2 finished! INFO @ Fri, 10 Dec 2021 12:19:41: #2 predicted fragment length is 39 bps INFO @ Fri, 10 Dec 2021 12:19:41: #2 alternative fragment length(s) may be 39 bps INFO @ Fri, 10 Dec 2021 12:19:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.10_model.r WARNING @ Fri, 10 Dec 2021 12:19:41: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:19:41: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Fri, 10 Dec 2021 12:19:41: #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 12:19:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:19:44: 17000000 INFO @ Fri, 10 Dec 2021 12:19:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:19:50: 18000000 INFO @ Fri, 10 Dec 2021 12:19:55: 19000000 INFO @ Fri, 10 Dec 2021 12:19:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:19:57: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:19:57: #1 total tags in treatment: 19466677 INFO @ Fri, 10 Dec 2021 12:19:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:19:57: #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 12:19:57: #1 tags after filtering in treatment: 19466677 INFO @ Fri, 10 Dec 2021 12:19:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:19:57: #1 finished! INFO @ Fri, 10 Dec 2021 12:19:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:19:59: #2 number of paired peaks: 209 WARNING @ Fri, 10 Dec 2021 12:19:59: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 10 Dec 2021 12:19:59: start model_add_line... INFO @ Fri, 10 Dec 2021 12:19:59: start X-correlation... INFO @ Fri, 10 Dec 2021 12:19:59: end of X-cor INFO @ Fri, 10 Dec 2021 12:19:59: #2 finished! INFO @ Fri, 10 Dec 2021 12:19:59: #2 predicted fragment length is 39 bps INFO @ Fri, 10 Dec 2021 12:19:59: #2 alternative fragment length(s) may be 39 bps INFO @ Fri, 10 Dec 2021 12:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.20_model.r WARNING @ Fri, 10 Dec 2021 12:19:59: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:19:59: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Fri, 10 Dec 2021 12:19:59: #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 12:19:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:19:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:20:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.05_summits.bed INFO @ Fri, 10 Dec 2021 12:20:02: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2108 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:20:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:20:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:20:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:20:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.10_summits.bed INFO @ Fri, 10 Dec 2021 12:20:31: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1560 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:20:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688937/SRX8688937.20_summits.bed INFO @ Fri, 10 Dec 2021 12:20:49: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1162 records, 4 fields): 6 millis CompletedMACS2peakCalling