Job ID = 6509146 SRX = SRX685467 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:29:23 prefetch.2.10.7: 1) Downloading 'SRR1556389'... 2020-06-26T15:29:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:33:12 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:33:12 prefetch.2.10.7: 1) 'SRR1556389' was downloaded successfully Read 45595988 spots for SRR1556389/SRR1556389.sra Written 45595988 spots for SRR1556389/SRR1556389.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: 00:14:10 45595988 reads; of these: 45595988 (100.00%) were unpaired; of these: 1735933 (3.81%) aligned 0 times 27915672 (61.22%) aligned exactly 1 time 15944383 (34.97%) aligned >1 times 96.19% overall alignment rate Time searching: 00:14:10 Overall time: 00:14:10 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 20 files... [bam_rmdupse_core] 11455777 / 43860055 = 0.2612 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 @ Sat, 27 Jun 2020 00:58:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.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 @ Sat, 27 Jun 2020 00:58:45: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:58:45: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:58:51: 1000000 INFO @ Sat, 27 Jun 2020 00:58:57: 2000000 INFO @ Sat, 27 Jun 2020 00:59:03: 3000000 INFO @ Sat, 27 Jun 2020 00:59:09: 4000000 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 @ Sat, 27 Jun 2020 00:59:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.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 @ Sat, 27 Jun 2020 00:59:15: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:59:15: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:59:15: 5000000 INFO @ Sat, 27 Jun 2020 00:59:21: 1000000 INFO @ Sat, 27 Jun 2020 00:59:21: 6000000 INFO @ Sat, 27 Jun 2020 00:59:26: 2000000 INFO @ Sat, 27 Jun 2020 00:59:27: 7000000 INFO @ Sat, 27 Jun 2020 00:59:32: 3000000 INFO @ Sat, 27 Jun 2020 00:59:33: 8000000 INFO @ Sat, 27 Jun 2020 00:59:38: 4000000 INFO @ Sat, 27 Jun 2020 00:59:39: 9000000 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 @ Sat, 27 Jun 2020 00:59:43: 5000000 INFO @ Sat, 27 Jun 2020 00:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.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 @ Sat, 27 Jun 2020 00:59:45: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:59:45: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:59:45: 10000000 INFO @ Sat, 27 Jun 2020 00:59:49: 6000000 INFO @ Sat, 27 Jun 2020 00:59:51: 1000000 INFO @ Sat, 27 Jun 2020 00:59:51: 11000000 INFO @ Sat, 27 Jun 2020 00:59:55: 7000000 INFO @ Sat, 27 Jun 2020 00:59:57: 2000000 INFO @ Sat, 27 Jun 2020 00:59:57: 12000000 INFO @ Sat, 27 Jun 2020 01:00:00: 8000000 INFO @ Sat, 27 Jun 2020 01:00:02: 3000000 INFO @ Sat, 27 Jun 2020 01:00:04: 13000000 INFO @ Sat, 27 Jun 2020 01:00:06: 9000000 INFO @ Sat, 27 Jun 2020 01:00:08: 4000000 INFO @ Sat, 27 Jun 2020 01:00:10: 14000000 INFO @ Sat, 27 Jun 2020 01:00:12: 10000000 INFO @ Sat, 27 Jun 2020 01:00:14: 5000000 INFO @ Sat, 27 Jun 2020 01:00:16: 15000000 INFO @ Sat, 27 Jun 2020 01:00:18: 11000000 INFO @ Sat, 27 Jun 2020 01:00:20: 6000000 INFO @ Sat, 27 Jun 2020 01:00:22: 16000000 INFO @ Sat, 27 Jun 2020 01:00:23: 12000000 INFO @ Sat, 27 Jun 2020 01:00:25: 7000000 INFO @ Sat, 27 Jun 2020 01:00:28: 17000000 INFO @ Sat, 27 Jun 2020 01:00:29: 13000000 INFO @ Sat, 27 Jun 2020 01:00:31: 8000000 INFO @ Sat, 27 Jun 2020 01:00:34: 18000000 INFO @ Sat, 27 Jun 2020 01:00:35: 14000000 INFO @ Sat, 27 Jun 2020 01:00:37: 9000000 INFO @ Sat, 27 Jun 2020 01:00:40: 19000000 INFO @ Sat, 27 Jun 2020 01:00:41: 15000000 INFO @ Sat, 27 Jun 2020 01:00:43: 10000000 INFO @ Sat, 27 Jun 2020 01:00:46: 20000000 INFO @ Sat, 27 Jun 2020 01:00:46: 16000000 INFO @ Sat, 27 Jun 2020 01:00:48: 11000000 INFO @ Sat, 27 Jun 2020 01:00:52: 17000000 INFO @ Sat, 27 Jun 2020 01:00:52: 21000000 INFO @ Sat, 27 Jun 2020 01:00:54: 12000000 INFO @ Sat, 27 Jun 2020 01:00:58: 18000000 INFO @ Sat, 27 Jun 2020 01:00:58: 22000000 INFO @ Sat, 27 Jun 2020 01:01:00: 13000000 INFO @ Sat, 27 Jun 2020 01:01:04: 19000000 INFO @ Sat, 27 Jun 2020 01:01:04: 23000000 INFO @ Sat, 27 Jun 2020 01:01:05: 14000000 INFO @ Sat, 27 Jun 2020 01:01:09: 20000000 INFO @ Sat, 27 Jun 2020 01:01:10: 24000000 INFO @ Sat, 27 Jun 2020 01:01:11: 15000000 INFO @ Sat, 27 Jun 2020 01:01:15: 21000000 INFO @ Sat, 27 Jun 2020 01:01:17: 25000000 INFO @ Sat, 27 Jun 2020 01:01:17: 16000000 INFO @ Sat, 27 Jun 2020 01:01:21: 22000000 INFO @ Sat, 27 Jun 2020 01:01:23: 26000000 INFO @ Sat, 27 Jun 2020 01:01:23: 17000000 INFO @ Sat, 27 Jun 2020 01:01:26: 23000000 INFO @ Sat, 27 Jun 2020 01:01:28: 18000000 INFO @ Sat, 27 Jun 2020 01:01:29: 27000000 INFO @ Sat, 27 Jun 2020 01:01:32: 24000000 INFO @ Sat, 27 Jun 2020 01:01:34: 19000000 INFO @ Sat, 27 Jun 2020 01:01:35: 28000000 INFO @ Sat, 27 Jun 2020 01:01:38: 25000000 INFO @ Sat, 27 Jun 2020 01:01:40: 20000000 INFO @ Sat, 27 Jun 2020 01:01:41: 29000000 INFO @ Sat, 27 Jun 2020 01:01:43: 26000000 INFO @ Sat, 27 Jun 2020 01:01:45: 21000000 INFO @ Sat, 27 Jun 2020 01:01:47: 30000000 INFO @ Sat, 27 Jun 2020 01:01:49: 27000000 INFO @ Sat, 27 Jun 2020 01:01:51: 22000000 INFO @ Sat, 27 Jun 2020 01:01:53: 31000000 INFO @ Sat, 27 Jun 2020 01:01:55: 28000000 INFO @ Sat, 27 Jun 2020 01:01:57: 23000000 INFO @ Sat, 27 Jun 2020 01:02:00: 32000000 INFO @ Sat, 27 Jun 2020 01:02:01: 29000000 INFO @ Sat, 27 Jun 2020 01:02:02: 24000000 INFO @ Sat, 27 Jun 2020 01:02:02: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 01:02:02: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 01:02:02: #1 total tags in treatment: 32404278 INFO @ Sat, 27 Jun 2020 01:02:02: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 01:02:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 01:02:03: #1 tags after filtering in treatment: 32404223 INFO @ Sat, 27 Jun 2020 01:02:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 01:02:03: #1 finished! INFO @ Sat, 27 Jun 2020 01:02:03: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 01:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 01:02:05: #2 number of paired peaks: 909 WARNING @ Sat, 27 Jun 2020 01:02:05: Fewer paired peaks (909) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 909 pairs to build model! INFO @ Sat, 27 Jun 2020 01:02:05: start model_add_line... INFO @ Sat, 27 Jun 2020 01:02:06: start X-correlation... INFO @ Sat, 27 Jun 2020 01:02:06: end of X-cor INFO @ Sat, 27 Jun 2020 01:02:06: #2 finished! INFO @ Sat, 27 Jun 2020 01:02:06: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 01:02:06: #2 alternative fragment length(s) may be 1,39 bps INFO @ Sat, 27 Jun 2020 01:02:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.05_model.r WARNING @ Sat, 27 Jun 2020 01:02:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 01:02:06: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Sat, 27 Jun 2020 01:02:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 01:02:06: #3 Call peaks... INFO @ Sat, 27 Jun 2020 01:02:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 01:02:06: 30000000 INFO @ Sat, 27 Jun 2020 01:02:08: 25000000 INFO @ Sat, 27 Jun 2020 01:02:12: 31000000 INFO @ Sat, 27 Jun 2020 01:02:13: 26000000 INFO @ Sat, 27 Jun 2020 01:02:18: 32000000 INFO @ Sat, 27 Jun 2020 01:02:19: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 01:02:20: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 01:02:20: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 01:02:20: #1 total tags in treatment: 32404278 INFO @ Sat, 27 Jun 2020 01:02:20: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 01:02:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 01:02:21: #1 tags after filtering in treatment: 32404223 INFO @ Sat, 27 Jun 2020 01:02:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 01:02:21: #1 finished! INFO @ Sat, 27 Jun 2020 01:02:21: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 01:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 01:02:23: #2 number of paired peaks: 909 WARNING @ Sat, 27 Jun 2020 01:02:23: Fewer paired peaks (909) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 909 pairs to build model! INFO @ Sat, 27 Jun 2020 01:02:23: start model_add_line... INFO @ Sat, 27 Jun 2020 01:02:23: start X-correlation... INFO @ Sat, 27 Jun 2020 01:02:23: end of X-cor INFO @ Sat, 27 Jun 2020 01:02:23: #2 finished! INFO @ Sat, 27 Jun 2020 01:02:23: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 01:02:23: #2 alternative fragment length(s) may be 1,39 bps INFO @ Sat, 27 Jun 2020 01:02:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.10_model.r WARNING @ Sat, 27 Jun 2020 01:02:23: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 01:02:23: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Sat, 27 Jun 2020 01:02:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 01:02:23: #3 Call peaks... INFO @ Sat, 27 Jun 2020 01:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 01:02:24: 28000000 INFO @ Sat, 27 Jun 2020 01:02:30: 29000000 INFO @ Sat, 27 Jun 2020 01:02:35: 30000000 INFO @ Sat, 27 Jun 2020 01:02:40: 31000000 INFO @ Sat, 27 Jun 2020 01:02:45: 32000000 INFO @ Sat, 27 Jun 2020 01:02:47: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 01:02:47: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 01:02:47: #1 total tags in treatment: 32404278 INFO @ Sat, 27 Jun 2020 01:02:47: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 01:02:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 01:02:48: #1 tags after filtering in treatment: 32404223 INFO @ Sat, 27 Jun 2020 01:02:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 01:02:48: #1 finished! INFO @ Sat, 27 Jun 2020 01:02:48: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 01:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 01:02:50: #2 number of paired peaks: 909 WARNING @ Sat, 27 Jun 2020 01:02:50: Fewer paired peaks (909) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 909 pairs to build model! INFO @ Sat, 27 Jun 2020 01:02:50: start model_add_line... INFO @ Sat, 27 Jun 2020 01:02:51: start X-correlation... INFO @ Sat, 27 Jun 2020 01:02:51: end of X-cor INFO @ Sat, 27 Jun 2020 01:02:51: #2 finished! INFO @ Sat, 27 Jun 2020 01:02:51: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 01:02:51: #2 alternative fragment length(s) may be 1,39 bps INFO @ Sat, 27 Jun 2020 01:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.20_model.r WARNING @ Sat, 27 Jun 2020 01:02:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 01:02:51: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Sat, 27 Jun 2020 01:02:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 01:02:51: #3 Call peaks... INFO @ Sat, 27 Jun 2020 01:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 01:02:53: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 01:03:09: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 01:03:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.05_peaks.xls INFO @ Sat, 27 Jun 2020 01:03:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 01:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.05_summits.bed INFO @ Sat, 27 Jun 2020 01:03:13: 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 @ Sat, 27 Jun 2020 01:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.10_peaks.xls INFO @ Sat, 27 Jun 2020 01:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 01:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.10_summits.bed INFO @ Sat, 27 Jun 2020 01:03:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 01:03:38: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 01:03:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.20_peaks.xls INFO @ Sat, 27 Jun 2020 01:03:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 01:03:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX685467/SRX685467.20_summits.bed INFO @ Sat, 27 Jun 2020 01:03:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling