Job ID = 10165795 SRX = SRX2765811 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 41952663 spots for SRR5482398/SRR5482398.sra Written 41952663 spots for SRR5482398/SRR5482398.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166190 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:37 41952663 reads; of these: 41952663 (100.00%) were unpaired; of these: 6783654 (16.17%) aligned 0 times 21344625 (50.88%) aligned exactly 1 time 13824384 (32.95%) aligned >1 times 83.83% overall alignment rate Time searching: 00:13:38 Overall time: 00:13:38 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 16 files... [bam_rmdupse_core] 6917396 / 35169009 = 0.1967 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:17:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.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 @ Thu, 08 Oct 2020 20:17:07: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:17:07: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:17:12: 1000000 INFO @ Thu, 08 Oct 2020 20:17:17: 2000000 INFO @ Thu, 08 Oct 2020 20:17:22: 3000000 INFO @ Thu, 08 Oct 2020 20:17:27: 4000000 INFO @ Thu, 08 Oct 2020 20:17:31: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:17:36: 6000000 INFO @ Thu, 08 Oct 2020 20:17:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.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 @ Thu, 08 Oct 2020 20:17:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:17:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:17:41: 7000000 INFO @ Thu, 08 Oct 2020 20:17:44: 1000000 INFO @ Thu, 08 Oct 2020 20:17:46: 8000000 INFO @ Thu, 08 Oct 2020 20:17:49: 2000000 INFO @ Thu, 08 Oct 2020 20:17:51: 9000000 INFO @ Thu, 08 Oct 2020 20:17:54: 3000000 INFO @ Thu, 08 Oct 2020 20:17:55: 10000000 INFO @ Thu, 08 Oct 2020 20:17:58: 4000000 INFO @ Thu, 08 Oct 2020 20:18:00: 11000000 INFO @ Thu, 08 Oct 2020 20:18:03: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:18:05: 12000000 INFO @ Thu, 08 Oct 2020 20:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.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 @ Thu, 08 Oct 2020 20:18:08: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:18:08: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:18:08: 6000000 INFO @ Thu, 08 Oct 2020 20:18:10: 13000000 INFO @ Thu, 08 Oct 2020 20:18:13: 1000000 INFO @ Thu, 08 Oct 2020 20:18:13: 7000000 INFO @ Thu, 08 Oct 2020 20:18:15: 14000000 INFO @ Thu, 08 Oct 2020 20:18:18: 2000000 INFO @ Thu, 08 Oct 2020 20:18:18: 8000000 INFO @ Thu, 08 Oct 2020 20:18:20: 15000000 INFO @ Thu, 08 Oct 2020 20:18:23: 9000000 INFO @ Thu, 08 Oct 2020 20:18:23: 3000000 INFO @ Thu, 08 Oct 2020 20:18:25: 16000000 INFO @ Thu, 08 Oct 2020 20:18:28: 10000000 INFO @ Thu, 08 Oct 2020 20:18:28: 4000000 INFO @ Thu, 08 Oct 2020 20:18:30: 17000000 INFO @ Thu, 08 Oct 2020 20:18:33: 11000000 INFO @ Thu, 08 Oct 2020 20:18:33: 5000000 INFO @ Thu, 08 Oct 2020 20:18:35: 18000000 INFO @ Thu, 08 Oct 2020 20:18:38: 12000000 INFO @ Thu, 08 Oct 2020 20:18:38: 6000000 INFO @ Thu, 08 Oct 2020 20:18:40: 19000000 INFO @ Thu, 08 Oct 2020 20:18:43: 7000000 INFO @ Thu, 08 Oct 2020 20:18:43: 13000000 INFO @ Thu, 08 Oct 2020 20:18:45: 20000000 INFO @ Thu, 08 Oct 2020 20:18:48: 8000000 INFO @ Thu, 08 Oct 2020 20:18:48: 14000000 INFO @ Thu, 08 Oct 2020 20:18:50: 21000000 INFO @ Thu, 08 Oct 2020 20:18:53: 9000000 INFO @ Thu, 08 Oct 2020 20:18:53: 15000000 INFO @ Thu, 08 Oct 2020 20:18:55: 22000000 INFO @ Thu, 08 Oct 2020 20:18:58: 10000000 INFO @ Thu, 08 Oct 2020 20:18:58: 16000000 INFO @ Thu, 08 Oct 2020 20:19:00: 23000000 INFO @ Thu, 08 Oct 2020 20:19:03: 11000000 INFO @ Thu, 08 Oct 2020 20:19:03: 17000000 INFO @ Thu, 08 Oct 2020 20:19:05: 24000000 INFO @ Thu, 08 Oct 2020 20:19:08: 12000000 INFO @ Thu, 08 Oct 2020 20:19:08: 18000000 INFO @ Thu, 08 Oct 2020 20:19:10: 25000000 INFO @ Thu, 08 Oct 2020 20:19:13: 13000000 INFO @ Thu, 08 Oct 2020 20:19:13: 19000000 INFO @ Thu, 08 Oct 2020 20:19:15: 26000000 INFO @ Thu, 08 Oct 2020 20:19:18: 14000000 INFO @ Thu, 08 Oct 2020 20:19:18: 20000000 INFO @ Thu, 08 Oct 2020 20:19:20: 27000000 INFO @ Thu, 08 Oct 2020 20:19:22: 15000000 INFO @ Thu, 08 Oct 2020 20:19:23: 21000000 INFO @ Thu, 08 Oct 2020 20:19:25: 28000000 INFO @ Thu, 08 Oct 2020 20:19:26: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:19:26: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:19:26: #1 total tags in treatment: 28251613 INFO @ Thu, 08 Oct 2020 20:19:26: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:19:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:19:27: #1 tags after filtering in treatment: 28251613 INFO @ Thu, 08 Oct 2020 20:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:19:27: #1 finished! INFO @ Thu, 08 Oct 2020 20:19:27: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:19:27: 16000000 INFO @ Thu, 08 Oct 2020 20:19:28: 22000000 INFO @ Thu, 08 Oct 2020 20:19:28: #2 number of paired peaks: 344 WARNING @ Thu, 08 Oct 2020 20:19:28: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Thu, 08 Oct 2020 20:19:28: start model_add_line... INFO @ Thu, 08 Oct 2020 20:19:29: start X-correlation... INFO @ Thu, 08 Oct 2020 20:19:29: end of X-cor INFO @ Thu, 08 Oct 2020 20:19:29: #2 finished! INFO @ Thu, 08 Oct 2020 20:19:29: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:19:29: #2 alternative fragment length(s) may be 1,44,562,592,598 bps INFO @ Thu, 08 Oct 2020 20:19:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05_model.r WARNING @ Thu, 08 Oct 2020 20:19:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:19:29: #2 You may need to consider one of the other alternative d(s): 1,44,562,592,598 WARNING @ Thu, 08 Oct 2020 20:19:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:19:29: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:19:32: 17000000 INFO @ Thu, 08 Oct 2020 20:19:32: 23000000 INFO @ Thu, 08 Oct 2020 20:19:37: 18000000 INFO @ Thu, 08 Oct 2020 20:19:37: 24000000 INFO @ Thu, 08 Oct 2020 20:19:42: 19000000 INFO @ Thu, 08 Oct 2020 20:19:42: 25000000 INFO @ Thu, 08 Oct 2020 20:19:47: 26000000 INFO @ Thu, 08 Oct 2020 20:19:47: 20000000 INFO @ Thu, 08 Oct 2020 20:19:52: 27000000 INFO @ Thu, 08 Oct 2020 20:19:52: 21000000 INFO @ Thu, 08 Oct 2020 20:19:57: 28000000 INFO @ Thu, 08 Oct 2020 20:19:57: 22000000 INFO @ Thu, 08 Oct 2020 20:19:58: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:19:58: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:19:58: #1 total tags in treatment: 28251613 INFO @ Thu, 08 Oct 2020 20:19:58: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:19:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:19:59: #1 tags after filtering in treatment: 28251613 INFO @ Thu, 08 Oct 2020 20:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:19:59: #1 finished! INFO @ Thu, 08 Oct 2020 20:19:59: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:20:00: #2 number of paired peaks: 344 WARNING @ Thu, 08 Oct 2020 20:20:00: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Thu, 08 Oct 2020 20:20:00: start model_add_line... INFO @ Thu, 08 Oct 2020 20:20:01: start X-correlation... INFO @ Thu, 08 Oct 2020 20:20:01: end of X-cor INFO @ Thu, 08 Oct 2020 20:20:01: #2 finished! INFO @ Thu, 08 Oct 2020 20:20:01: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:20:01: #2 alternative fragment length(s) may be 1,44,562,592,598 bps INFO @ Thu, 08 Oct 2020 20:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10_model.r WARNING @ Thu, 08 Oct 2020 20:20:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:20:01: #2 You may need to consider one of the other alternative d(s): 1,44,562,592,598 WARNING @ Thu, 08 Oct 2020 20:20:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:20:01: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:20:02: 23000000 INFO @ Thu, 08 Oct 2020 20:20:07: 24000000 INFO @ Thu, 08 Oct 2020 20:20:12: 25000000 INFO @ Thu, 08 Oct 2020 20:20:14: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:20:17: 26000000 INFO @ Thu, 08 Oct 2020 20:20:21: 27000000 INFO @ Thu, 08 Oct 2020 20:20:26: 28000000 INFO @ Thu, 08 Oct 2020 20:20:27: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:20:27: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:20:27: #1 total tags in treatment: 28251613 INFO @ Thu, 08 Oct 2020 20:20:27: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:20:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:20:28: #1 tags after filtering in treatment: 28251613 INFO @ Thu, 08 Oct 2020 20:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:20:28: #1 finished! INFO @ Thu, 08 Oct 2020 20:20:28: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:20:30: #2 number of paired peaks: 344 WARNING @ Thu, 08 Oct 2020 20:20:30: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Thu, 08 Oct 2020 20:20:30: start model_add_line... INFO @ Thu, 08 Oct 2020 20:20:30: start X-correlation... INFO @ Thu, 08 Oct 2020 20:20:30: end of X-cor INFO @ Thu, 08 Oct 2020 20:20:30: #2 finished! INFO @ Thu, 08 Oct 2020 20:20:30: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:20:30: #2 alternative fragment length(s) may be 1,44,562,592,598 bps INFO @ Thu, 08 Oct 2020 20:20:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20_model.r WARNING @ Thu, 08 Oct 2020 20:20:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:20:30: #2 You may need to consider one of the other alternative d(s): 1,44,562,592,598 WARNING @ Thu, 08 Oct 2020 20:20:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:20:30: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:20:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:20:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:20:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:20:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05_summits.bed INFO @ Thu, 08 Oct 2020 20:20:34: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:20:46: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10_summits.bed INFO @ Thu, 08 Oct 2020 20:21:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:21:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20_summits.bed INFO @ Thu, 08 Oct 2020 20:21:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling