Job ID = 6528388 SRX = SRX5661490 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:59:14 prefetch.2.10.7: 1) Downloading 'SRR8874497'... 2020-06-29T14:59:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:03:19 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:03:19 prefetch.2.10.7: 1) 'SRR8874497' was downloaded successfully 2020-06-29T15:03:19 prefetch.2.10.7: 'SRR8874497' has 0 unresolved dependencies Read 38887199 spots for SRR8874497/SRR8874497.sra Written 38887199 spots for SRR8874497/SRR8874497.sra 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: 00:18:52 38887199 reads; of these: 38887199 (100.00%) were unpaired; of these: 955373 (2.46%) aligned 0 times 16034380 (41.23%) aligned exactly 1 time 21897446 (56.31%) aligned >1 times 97.54% overall alignment rate Time searching: 00:18:52 Overall time: 00:18:52 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] 11569852 / 37931826 = 0.3050 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 @ Tue, 30 Jun 2020 00:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.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 @ Tue, 30 Jun 2020 00:43:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:43:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:43:11: 1000000 INFO @ Tue, 30 Jun 2020 00:43:18: 2000000 INFO @ Tue, 30 Jun 2020 00:43:26: 3000000 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 @ Tue, 30 Jun 2020 00:43:32: 4000000 INFO @ Tue, 30 Jun 2020 00:43:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.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 @ Tue, 30 Jun 2020 00:43:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:43:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:43:39: 5000000 INFO @ Tue, 30 Jun 2020 00:43:41: 1000000 INFO @ Tue, 30 Jun 2020 00:43:46: 6000000 INFO @ Tue, 30 Jun 2020 00:43:47: 2000000 INFO @ Tue, 30 Jun 2020 00:43:52: 7000000 INFO @ Tue, 30 Jun 2020 00:43:53: 3000000 INFO @ Tue, 30 Jun 2020 00:43:59: 8000000 INFO @ Tue, 30 Jun 2020 00:44:00: 4000000 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 @ Tue, 30 Jun 2020 00:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.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 @ Tue, 30 Jun 2020 00:44:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:44:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:44:06: 9000000 INFO @ Tue, 30 Jun 2020 00:44:06: 5000000 INFO @ Tue, 30 Jun 2020 00:44:11: 1000000 INFO @ Tue, 30 Jun 2020 00:44:13: 6000000 INFO @ Tue, 30 Jun 2020 00:44:13: 10000000 INFO @ Tue, 30 Jun 2020 00:44:18: 2000000 INFO @ Tue, 30 Jun 2020 00:44:19: 7000000 INFO @ Tue, 30 Jun 2020 00:44:20: 11000000 INFO @ Tue, 30 Jun 2020 00:44:25: 3000000 INFO @ Tue, 30 Jun 2020 00:44:26: 8000000 INFO @ Tue, 30 Jun 2020 00:44:27: 12000000 INFO @ Tue, 30 Jun 2020 00:44:32: 4000000 INFO @ Tue, 30 Jun 2020 00:44:32: 9000000 INFO @ Tue, 30 Jun 2020 00:44:34: 13000000 INFO @ Tue, 30 Jun 2020 00:44:39: 10000000 INFO @ Tue, 30 Jun 2020 00:44:39: 5000000 INFO @ Tue, 30 Jun 2020 00:44:41: 14000000 INFO @ Tue, 30 Jun 2020 00:44:45: 11000000 INFO @ Tue, 30 Jun 2020 00:44:46: 6000000 INFO @ Tue, 30 Jun 2020 00:44:48: 15000000 INFO @ Tue, 30 Jun 2020 00:44:52: 12000000 INFO @ Tue, 30 Jun 2020 00:44:53: 7000000 INFO @ Tue, 30 Jun 2020 00:44:55: 16000000 INFO @ Tue, 30 Jun 2020 00:44:58: 13000000 INFO @ Tue, 30 Jun 2020 00:45:00: 8000000 INFO @ Tue, 30 Jun 2020 00:45:02: 17000000 INFO @ Tue, 30 Jun 2020 00:45:05: 14000000 INFO @ Tue, 30 Jun 2020 00:45:07: 9000000 INFO @ Tue, 30 Jun 2020 00:45:10: 18000000 INFO @ Tue, 30 Jun 2020 00:45:12: 15000000 INFO @ Tue, 30 Jun 2020 00:45:14: 10000000 INFO @ Tue, 30 Jun 2020 00:45:17: 19000000 INFO @ Tue, 30 Jun 2020 00:45:18: 16000000 INFO @ Tue, 30 Jun 2020 00:45:21: 11000000 INFO @ Tue, 30 Jun 2020 00:45:24: 20000000 INFO @ Tue, 30 Jun 2020 00:45:25: 17000000 INFO @ Tue, 30 Jun 2020 00:45:28: 12000000 INFO @ Tue, 30 Jun 2020 00:45:31: 21000000 INFO @ Tue, 30 Jun 2020 00:45:31: 18000000 INFO @ Tue, 30 Jun 2020 00:45:34: 13000000 INFO @ Tue, 30 Jun 2020 00:45:38: 22000000 INFO @ Tue, 30 Jun 2020 00:45:38: 19000000 INFO @ Tue, 30 Jun 2020 00:45:41: 14000000 INFO @ Tue, 30 Jun 2020 00:45:45: 20000000 INFO @ Tue, 30 Jun 2020 00:45:45: 23000000 INFO @ Tue, 30 Jun 2020 00:45:48: 15000000 INFO @ Tue, 30 Jun 2020 00:45:51: 21000000 INFO @ Tue, 30 Jun 2020 00:45:52: 24000000 INFO @ Tue, 30 Jun 2020 00:45:56: 16000000 INFO @ Tue, 30 Jun 2020 00:45:58: 22000000 INFO @ Tue, 30 Jun 2020 00:45:59: 25000000 INFO @ Tue, 30 Jun 2020 00:46:03: 17000000 INFO @ Tue, 30 Jun 2020 00:46:04: 23000000 INFO @ Tue, 30 Jun 2020 00:46:06: 26000000 INFO @ Tue, 30 Jun 2020 00:46:08: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:46:08: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:46:08: #1 total tags in treatment: 26361974 INFO @ Tue, 30 Jun 2020 00:46:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:46:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:46:09: #1 tags after filtering in treatment: 26361974 INFO @ Tue, 30 Jun 2020 00:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:46:09: #1 finished! INFO @ Tue, 30 Jun 2020 00:46:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:46:10: 18000000 INFO @ Tue, 30 Jun 2020 00:46:10: #2 number of paired peaks: 507 WARNING @ Tue, 30 Jun 2020 00:46:10: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Tue, 30 Jun 2020 00:46:10: start model_add_line... INFO @ Tue, 30 Jun 2020 00:46:11: 24000000 INFO @ Tue, 30 Jun 2020 00:46:11: start X-correlation... INFO @ Tue, 30 Jun 2020 00:46:11: end of X-cor INFO @ Tue, 30 Jun 2020 00:46:11: #2 finished! INFO @ Tue, 30 Jun 2020 00:46:11: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:46:11: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 30 Jun 2020 00:46:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.05_model.r WARNING @ Tue, 30 Jun 2020 00:46:11: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:46:11: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 30 Jun 2020 00:46:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:46:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:46:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:46:16: 19000000 INFO @ Tue, 30 Jun 2020 00:46:17: 25000000 INFO @ Tue, 30 Jun 2020 00:46:23: 20000000 INFO @ Tue, 30 Jun 2020 00:46:23: 26000000 INFO @ Tue, 30 Jun 2020 00:46:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:46:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:46:26: #1 total tags in treatment: 26361974 INFO @ Tue, 30 Jun 2020 00:46:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:46:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:46:26: #1 tags after filtering in treatment: 26361974 INFO @ Tue, 30 Jun 2020 00:46:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:46:26: #1 finished! INFO @ Tue, 30 Jun 2020 00:46:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:46:28: #2 number of paired peaks: 507 WARNING @ Tue, 30 Jun 2020 00:46:28: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Tue, 30 Jun 2020 00:46:28: start model_add_line... INFO @ Tue, 30 Jun 2020 00:46:28: start X-correlation... INFO @ Tue, 30 Jun 2020 00:46:28: end of X-cor INFO @ Tue, 30 Jun 2020 00:46:28: #2 finished! INFO @ Tue, 30 Jun 2020 00:46:28: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:46:28: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 30 Jun 2020 00:46:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.10_model.r WARNING @ Tue, 30 Jun 2020 00:46:28: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:46:28: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 30 Jun 2020 00:46:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:46:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:46:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:46:29: 21000000 INFO @ Tue, 30 Jun 2020 00:46:36: 22000000 INFO @ Tue, 30 Jun 2020 00:46:42: 23000000 INFO @ Tue, 30 Jun 2020 00:46:48: 24000000 INFO @ Tue, 30 Jun 2020 00:46:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:46:54: 25000000 INFO @ Tue, 30 Jun 2020 00:47:01: 26000000 INFO @ Tue, 30 Jun 2020 00:47:03: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:47:03: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:47:03: #1 total tags in treatment: 26361974 INFO @ Tue, 30 Jun 2020 00:47:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:47:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:47:04: #1 tags after filtering in treatment: 26361974 INFO @ Tue, 30 Jun 2020 00:47:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:47:04: #1 finished! INFO @ Tue, 30 Jun 2020 00:47:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:47:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:47:05: #2 number of paired peaks: 507 WARNING @ Tue, 30 Jun 2020 00:47:05: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Tue, 30 Jun 2020 00:47:05: start model_add_line... INFO @ Tue, 30 Jun 2020 00:47:06: start X-correlation... INFO @ Tue, 30 Jun 2020 00:47:06: end of X-cor INFO @ Tue, 30 Jun 2020 00:47:06: #2 finished! INFO @ Tue, 30 Jun 2020 00:47:06: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:47:06: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 30 Jun 2020 00:47:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.20_model.r WARNING @ Tue, 30 Jun 2020 00:47:06: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:47:06: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 30 Jun 2020 00:47:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:47:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:47:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:47:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.05_summits.bed INFO @ Tue, 30 Jun 2020 00:47:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:47:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:47:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:47:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.10_summits.bed INFO @ Tue, 30 Jun 2020 00:47:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:47:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:48:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:48:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:48:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661490/SRX5661490.20_summits.bed INFO @ Tue, 30 Jun 2020 00:48:03: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling