Job ID = 6454947 SRX = SRX2618494 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:34:40 prefetch.2.10.7: 1) Downloading 'SRR5319048'... 2020-06-21T09:34:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:38:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:38:30 prefetch.2.10.7: 1) 'SRR5319048' was downloaded successfully 2020-06-21T09:38:30 prefetch.2.10.7: 'SRR5319048' has 0 unresolved dependencies Read 44277745 spots for SRR5319048/SRR5319048.sra Written 44277745 spots for SRR5319048/SRR5319048.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: 00:11:48 44277745 reads; of these: 44277745 (100.00%) were unpaired; of these: 2272785 (5.13%) aligned 0 times 31699274 (71.59%) aligned exactly 1 time 10305686 (23.28%) aligned >1 times 94.87% overall alignment rate Time searching: 00:11:48 Overall time: 00:11:48 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] 7538785 / 42004960 = 0.1795 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 @ Sun, 21 Jun 2020 19:00:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.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 @ Sun, 21 Jun 2020 19:00:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:02: 1000000 INFO @ Sun, 21 Jun 2020 19:01:07: 2000000 INFO @ Sun, 21 Jun 2020 19:01:12: 3000000 INFO @ Sun, 21 Jun 2020 19:01:17: 4000000 INFO @ Sun, 21 Jun 2020 19:01:21: 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 @ Sun, 21 Jun 2020 19:01:26: 6000000 INFO @ Sun, 21 Jun 2020 19:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.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 @ Sun, 21 Jun 2020 19:01:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:31: 7000000 INFO @ Sun, 21 Jun 2020 19:01:33: 1000000 INFO @ Sun, 21 Jun 2020 19:01:36: 8000000 INFO @ Sun, 21 Jun 2020 19:01:38: 2000000 INFO @ Sun, 21 Jun 2020 19:01:41: 9000000 INFO @ Sun, 21 Jun 2020 19:01:43: 3000000 INFO @ Sun, 21 Jun 2020 19:01:46: 10000000 INFO @ Sun, 21 Jun 2020 19:01:48: 4000000 INFO @ Sun, 21 Jun 2020 19:01:51: 11000000 INFO @ Sun, 21 Jun 2020 19:01:53: 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 @ Sun, 21 Jun 2020 19:01:56: 12000000 INFO @ Sun, 21 Jun 2020 19:01:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.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 @ Sun, 21 Jun 2020 19:01:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:58: 6000000 INFO @ Sun, 21 Jun 2020 19:02:01: 13000000 INFO @ Sun, 21 Jun 2020 19:02:02: 1000000 INFO @ Sun, 21 Jun 2020 19:02:03: 7000000 INFO @ Sun, 21 Jun 2020 19:02:06: 14000000 INFO @ Sun, 21 Jun 2020 19:02:07: 2000000 INFO @ Sun, 21 Jun 2020 19:02:08: 8000000 INFO @ Sun, 21 Jun 2020 19:02:11: 15000000 INFO @ Sun, 21 Jun 2020 19:02:13: 3000000 INFO @ Sun, 21 Jun 2020 19:02:13: 9000000 INFO @ Sun, 21 Jun 2020 19:02:16: 16000000 INFO @ Sun, 21 Jun 2020 19:02:18: 4000000 INFO @ Sun, 21 Jun 2020 19:02:18: 10000000 INFO @ Sun, 21 Jun 2020 19:02:22: 17000000 INFO @ Sun, 21 Jun 2020 19:02:23: 5000000 INFO @ Sun, 21 Jun 2020 19:02:23: 11000000 INFO @ Sun, 21 Jun 2020 19:02:27: 18000000 INFO @ Sun, 21 Jun 2020 19:02:28: 6000000 INFO @ Sun, 21 Jun 2020 19:02:29: 12000000 INFO @ Sun, 21 Jun 2020 19:02:32: 19000000 INFO @ Sun, 21 Jun 2020 19:02:33: 7000000 INFO @ Sun, 21 Jun 2020 19:02:34: 13000000 INFO @ Sun, 21 Jun 2020 19:02:37: 20000000 INFO @ Sun, 21 Jun 2020 19:02:38: 8000000 INFO @ Sun, 21 Jun 2020 19:02:39: 14000000 INFO @ Sun, 21 Jun 2020 19:02:42: 21000000 INFO @ Sun, 21 Jun 2020 19:02:43: 9000000 INFO @ Sun, 21 Jun 2020 19:02:44: 15000000 INFO @ Sun, 21 Jun 2020 19:02:47: 22000000 INFO @ Sun, 21 Jun 2020 19:02:48: 10000000 INFO @ Sun, 21 Jun 2020 19:02:49: 16000000 INFO @ Sun, 21 Jun 2020 19:02:53: 23000000 INFO @ Sun, 21 Jun 2020 19:02:54: 11000000 INFO @ Sun, 21 Jun 2020 19:02:54: 17000000 INFO @ Sun, 21 Jun 2020 19:02:58: 24000000 INFO @ Sun, 21 Jun 2020 19:02:59: 12000000 INFO @ Sun, 21 Jun 2020 19:02:59: 18000000 INFO @ Sun, 21 Jun 2020 19:03:03: 25000000 INFO @ Sun, 21 Jun 2020 19:03:04: 13000000 INFO @ Sun, 21 Jun 2020 19:03:05: 19000000 INFO @ Sun, 21 Jun 2020 19:03:08: 26000000 INFO @ Sun, 21 Jun 2020 19:03:09: 14000000 INFO @ Sun, 21 Jun 2020 19:03:10: 20000000 INFO @ Sun, 21 Jun 2020 19:03:13: 27000000 INFO @ Sun, 21 Jun 2020 19:03:15: 15000000 INFO @ Sun, 21 Jun 2020 19:03:15: 21000000 INFO @ Sun, 21 Jun 2020 19:03:19: 28000000 INFO @ Sun, 21 Jun 2020 19:03:20: 16000000 INFO @ Sun, 21 Jun 2020 19:03:20: 22000000 INFO @ Sun, 21 Jun 2020 19:03:24: 29000000 INFO @ Sun, 21 Jun 2020 19:03:25: 17000000 INFO @ Sun, 21 Jun 2020 19:03:25: 23000000 INFO @ Sun, 21 Jun 2020 19:03:30: 30000000 INFO @ Sun, 21 Jun 2020 19:03:31: 18000000 INFO @ Sun, 21 Jun 2020 19:03:31: 24000000 INFO @ Sun, 21 Jun 2020 19:03:35: 31000000 INFO @ Sun, 21 Jun 2020 19:03:36: 19000000 INFO @ Sun, 21 Jun 2020 19:03:36: 25000000 INFO @ Sun, 21 Jun 2020 19:03:40: 32000000 INFO @ Sun, 21 Jun 2020 19:03:41: 20000000 INFO @ Sun, 21 Jun 2020 19:03:41: 26000000 INFO @ Sun, 21 Jun 2020 19:03:46: 33000000 INFO @ Sun, 21 Jun 2020 19:03:46: 27000000 INFO @ Sun, 21 Jun 2020 19:03:47: 21000000 INFO @ Sun, 21 Jun 2020 19:03:51: 34000000 INFO @ Sun, 21 Jun 2020 19:03:52: 28000000 INFO @ Sun, 21 Jun 2020 19:03:53: 22000000 INFO @ Sun, 21 Jun 2020 19:03:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:54: #1 total tags in treatment: 34466175 INFO @ Sun, 21 Jun 2020 19:03:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:03:55: #1 tags after filtering in treatment: 34466175 INFO @ Sun, 21 Jun 2020 19:03:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:57: #2 number of paired peaks: 229 WARNING @ Sun, 21 Jun 2020 19:03:57: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sun, 21 Jun 2020 19:03:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:58: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:03:58: #2 alternative fragment length(s) may be 1,12 bps INFO @ Sun, 21 Jun 2020 19:03:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.05_model.r WARNING @ Sun, 21 Jun 2020 19:03:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:03:58: #2 You may need to consider one of the other alternative d(s): 1,12 WARNING @ Sun, 21 Jun 2020 19:03:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:03:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:58: 29000000 INFO @ Sun, 21 Jun 2020 19:03:58: 23000000 INFO @ Sun, 21 Jun 2020 19:04:03: 30000000 INFO @ Sun, 21 Jun 2020 19:04:03: 24000000 INFO @ Sun, 21 Jun 2020 19:04:08: 31000000 INFO @ Sun, 21 Jun 2020 19:04:09: 25000000 INFO @ Sun, 21 Jun 2020 19:04:14: 32000000 INFO @ Sun, 21 Jun 2020 19:04:14: 26000000 INFO @ Sun, 21 Jun 2020 19:04:19: 33000000 INFO @ Sun, 21 Jun 2020 19:04:19: 27000000 INFO @ Sun, 21 Jun 2020 19:04:25: 34000000 INFO @ Sun, 21 Jun 2020 19:04:25: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:04:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:27: #1 total tags in treatment: 34466175 INFO @ Sun, 21 Jun 2020 19:04:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:04:28: #1 tags after filtering in treatment: 34466175 INFO @ Sun, 21 Jun 2020 19:04:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:30: 29000000 INFO @ Sun, 21 Jun 2020 19:04:30: #2 number of paired peaks: 229 WARNING @ Sun, 21 Jun 2020 19:04:30: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:31: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:04:31: #2 alternative fragment length(s) may be 1,12 bps INFO @ Sun, 21 Jun 2020 19:04:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.10_model.r WARNING @ Sun, 21 Jun 2020 19:04:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:31: #2 You may need to consider one of the other alternative d(s): 1,12 WARNING @ Sun, 21 Jun 2020 19:04:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:04:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:35: 30000000 INFO @ Sun, 21 Jun 2020 19:04:40: 31000000 INFO @ Sun, 21 Jun 2020 19:04:45: 32000000 INFO @ Sun, 21 Jun 2020 19:04:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:51: 33000000 INFO @ Sun, 21 Jun 2020 19:04:56: 34000000 INFO @ Sun, 21 Jun 2020 19:04:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:59: #1 total tags in treatment: 34466175 INFO @ Sun, 21 Jun 2020 19:04:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:04:59: #1 tags after filtering in treatment: 34466175 INFO @ Sun, 21 Jun 2020 19:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:02: #2 number of paired peaks: 229 WARNING @ Sun, 21 Jun 2020 19:05:02: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:02: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:05:02: #2 alternative fragment length(s) may be 1,12 bps INFO @ Sun, 21 Jun 2020 19:05:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.20_model.r WARNING @ Sun, 21 Jun 2020 19:05:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:05:02: #2 You may need to consider one of the other alternative d(s): 1,12 WARNING @ Sun, 21 Jun 2020 19:05:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:05:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.05_summits.bed INFO @ Sun, 21 Jun 2020 19:05:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:05:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618494/SRX2618494.20_summits.bed INFO @ Sun, 21 Jun 2020 19:06:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling