Job ID = 6527670 SRX = SRX201886 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:08:20 prefetch.2.10.7: 1) Downloading 'SRR609676'... 2020-06-29T13:08:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:16:32 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:16:32 prefetch.2.10.7: 1) 'SRR609676' was downloaded successfully Read 54947001 spots for SRR609676/SRR609676.sra Written 54947001 spots for SRR609676/SRR609676.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: 00:32:42 54947001 reads; of these: 54947001 (100.00%) were unpaired; of these: 866070 (1.58%) aligned 0 times 14168309 (25.79%) aligned exactly 1 time 39912622 (72.64%) aligned >1 times 98.42% overall alignment rate Time searching: 00:32:43 Overall time: 00:32:43 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 24 files... [bam_rmdupse_core] 24013400 / 54080931 = 0.4440 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 @ Mon, 29 Jun 2020 23:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.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 @ Mon, 29 Jun 2020 23:23:32: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:23:32: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:23:37: 1000000 INFO @ Mon, 29 Jun 2020 23:23:43: 2000000 INFO @ Mon, 29 Jun 2020 23:23:49: 3000000 INFO @ Mon, 29 Jun 2020 23:23:55: 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 @ Mon, 29 Jun 2020 23:24:00: 5000000 INFO @ Mon, 29 Jun 2020 23:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.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 @ Mon, 29 Jun 2020 23:24:02: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:24:02: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:24:06: 6000000 INFO @ Mon, 29 Jun 2020 23:24:09: 1000000 INFO @ Mon, 29 Jun 2020 23:24:12: 7000000 INFO @ Mon, 29 Jun 2020 23:24:15: 2000000 INFO @ Mon, 29 Jun 2020 23:24:19: 8000000 INFO @ Mon, 29 Jun 2020 23:24:22: 3000000 INFO @ Mon, 29 Jun 2020 23:24:25: 9000000 INFO @ Mon, 29 Jun 2020 23:24:28: 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 @ Mon, 29 Jun 2020 23:24:31: 10000000 INFO @ Mon, 29 Jun 2020 23:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.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 @ Mon, 29 Jun 2020 23:24:32: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:24:32: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:24:36: 5000000 INFO @ Mon, 29 Jun 2020 23:24:38: 11000000 INFO @ Mon, 29 Jun 2020 23:24:38: 1000000 INFO @ Mon, 29 Jun 2020 23:24:42: 6000000 INFO @ Mon, 29 Jun 2020 23:24:44: 12000000 INFO @ Mon, 29 Jun 2020 23:24:45: 2000000 INFO @ Mon, 29 Jun 2020 23:24:49: 7000000 INFO @ Mon, 29 Jun 2020 23:24:51: 13000000 INFO @ Mon, 29 Jun 2020 23:24:52: 3000000 INFO @ Mon, 29 Jun 2020 23:24:56: 8000000 INFO @ Mon, 29 Jun 2020 23:24:58: 14000000 INFO @ Mon, 29 Jun 2020 23:24:59: 4000000 INFO @ Mon, 29 Jun 2020 23:25:03: 9000000 INFO @ Mon, 29 Jun 2020 23:25:04: 15000000 INFO @ Mon, 29 Jun 2020 23:25:06: 5000000 INFO @ Mon, 29 Jun 2020 23:25:10: 10000000 INFO @ Mon, 29 Jun 2020 23:25:11: 16000000 INFO @ Mon, 29 Jun 2020 23:25:12: 6000000 INFO @ Mon, 29 Jun 2020 23:25:17: 11000000 INFO @ Mon, 29 Jun 2020 23:25:18: 17000000 INFO @ Mon, 29 Jun 2020 23:25:19: 7000000 INFO @ Mon, 29 Jun 2020 23:25:23: 12000000 INFO @ Mon, 29 Jun 2020 23:25:24: 18000000 INFO @ Mon, 29 Jun 2020 23:25:26: 8000000 INFO @ Mon, 29 Jun 2020 23:25:30: 13000000 INFO @ Mon, 29 Jun 2020 23:25:31: 19000000 INFO @ Mon, 29 Jun 2020 23:25:33: 9000000 INFO @ Mon, 29 Jun 2020 23:25:37: 14000000 INFO @ Mon, 29 Jun 2020 23:25:38: 20000000 INFO @ Mon, 29 Jun 2020 23:25:39: 10000000 INFO @ Mon, 29 Jun 2020 23:25:44: 15000000 INFO @ Mon, 29 Jun 2020 23:25:45: 21000000 INFO @ Mon, 29 Jun 2020 23:25:46: 11000000 INFO @ Mon, 29 Jun 2020 23:25:51: 16000000 INFO @ Mon, 29 Jun 2020 23:25:51: 22000000 INFO @ Mon, 29 Jun 2020 23:25:53: 12000000 INFO @ Mon, 29 Jun 2020 23:25:57: 17000000 INFO @ Mon, 29 Jun 2020 23:25:58: 23000000 INFO @ Mon, 29 Jun 2020 23:25:59: 13000000 INFO @ Mon, 29 Jun 2020 23:26:04: 18000000 INFO @ Mon, 29 Jun 2020 23:26:04: 24000000 INFO @ Mon, 29 Jun 2020 23:26:06: 14000000 INFO @ Mon, 29 Jun 2020 23:26:11: 19000000 INFO @ Mon, 29 Jun 2020 23:26:11: 25000000 INFO @ Mon, 29 Jun 2020 23:26:13: 15000000 INFO @ Mon, 29 Jun 2020 23:26:17: 26000000 INFO @ Mon, 29 Jun 2020 23:26:18: 20000000 INFO @ Mon, 29 Jun 2020 23:26:20: 16000000 INFO @ Mon, 29 Jun 2020 23:26:24: 27000000 INFO @ Mon, 29 Jun 2020 23:26:24: 21000000 INFO @ Mon, 29 Jun 2020 23:26:26: 17000000 INFO @ Mon, 29 Jun 2020 23:26:31: 28000000 INFO @ Mon, 29 Jun 2020 23:26:31: 22000000 INFO @ Mon, 29 Jun 2020 23:26:33: 18000000 INFO @ Mon, 29 Jun 2020 23:26:37: 29000000 INFO @ Mon, 29 Jun 2020 23:26:38: 23000000 INFO @ Mon, 29 Jun 2020 23:26:40: 19000000 INFO @ Mon, 29 Jun 2020 23:26:44: 30000000 INFO @ Mon, 29 Jun 2020 23:26:44: 24000000 INFO @ Mon, 29 Jun 2020 23:26:44: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:26:44: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:26:44: #1 total tags in treatment: 30067531 INFO @ Mon, 29 Jun 2020 23:26:44: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:26:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:26:45: #1 tags after filtering in treatment: 30067531 INFO @ Mon, 29 Jun 2020 23:26:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:26:45: #1 finished! INFO @ Mon, 29 Jun 2020 23:26:45: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:26:46: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:26:47: #2 number of paired peaks: 1468 INFO @ Mon, 29 Jun 2020 23:26:47: start model_add_line... INFO @ Mon, 29 Jun 2020 23:26:48: start X-correlation... INFO @ Mon, 29 Jun 2020 23:26:48: end of X-cor INFO @ Mon, 29 Jun 2020 23:26:48: #2 finished! INFO @ Mon, 29 Jun 2020 23:26:48: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:26:48: #2 alternative fragment length(s) may be 2,34 bps INFO @ Mon, 29 Jun 2020 23:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.05_model.r WARNING @ Mon, 29 Jun 2020 23:26:48: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:26:48: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Mon, 29 Jun 2020 23:26:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:26:48: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:26:50: 25000000 INFO @ Mon, 29 Jun 2020 23:26:52: 21000000 INFO @ Mon, 29 Jun 2020 23:26:56: 26000000 INFO @ Mon, 29 Jun 2020 23:26:58: 22000000 INFO @ Mon, 29 Jun 2020 23:27:03: 27000000 INFO @ Mon, 29 Jun 2020 23:27:04: 23000000 INFO @ Mon, 29 Jun 2020 23:27:09: 28000000 INFO @ Mon, 29 Jun 2020 23:27:10: 24000000 INFO @ Mon, 29 Jun 2020 23:27:15: 29000000 INFO @ Mon, 29 Jun 2020 23:27:17: 25000000 INFO @ Mon, 29 Jun 2020 23:27:21: 30000000 INFO @ Mon, 29 Jun 2020 23:27:22: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:27:22: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:27:22: #1 total tags in treatment: 30067531 INFO @ Mon, 29 Jun 2020 23:27:22: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:27:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:27:23: #1 tags after filtering in treatment: 30067531 INFO @ Mon, 29 Jun 2020 23:27:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:27:23: #1 finished! INFO @ Mon, 29 Jun 2020 23:27:23: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:27:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:27:23: 26000000 INFO @ Mon, 29 Jun 2020 23:27:25: #2 number of paired peaks: 1468 INFO @ Mon, 29 Jun 2020 23:27:25: start model_add_line... INFO @ Mon, 29 Jun 2020 23:27:25: start X-correlation... INFO @ Mon, 29 Jun 2020 23:27:25: end of X-cor INFO @ Mon, 29 Jun 2020 23:27:25: #2 finished! INFO @ Mon, 29 Jun 2020 23:27:25: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:27:25: #2 alternative fragment length(s) may be 2,34 bps INFO @ Mon, 29 Jun 2020 23:27:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.10_model.r WARNING @ Mon, 29 Jun 2020 23:27:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:27:25: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Mon, 29 Jun 2020 23:27:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:27:25: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:27:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:27:27: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:27:28: 27000000 INFO @ Mon, 29 Jun 2020 23:27:34: 28000000 INFO @ Mon, 29 Jun 2020 23:27:39: 29000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:27:45: 30000000 INFO @ Mon, 29 Jun 2020 23:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:27:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:27:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.05_summits.bed INFO @ Mon, 29 Jun 2020 23:27:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:27:46: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:27:46: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:27:46: #1 total tags in treatment: 30067531 INFO @ Mon, 29 Jun 2020 23:27:46: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:27:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:27:46: #1 tags after filtering in treatment: 30067531 INFO @ Mon, 29 Jun 2020 23:27:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:27:46: #1 finished! INFO @ Mon, 29 Jun 2020 23:27:46: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:27:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:27:48: #2 number of paired peaks: 1468 INFO @ Mon, 29 Jun 2020 23:27:48: start model_add_line... INFO @ Mon, 29 Jun 2020 23:27:49: start X-correlation... INFO @ Mon, 29 Jun 2020 23:27:49: end of X-cor INFO @ Mon, 29 Jun 2020 23:27:49: #2 finished! INFO @ Mon, 29 Jun 2020 23:27:49: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:27:49: #2 alternative fragment length(s) may be 2,34 bps INFO @ Mon, 29 Jun 2020 23:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.20_model.r WARNING @ Mon, 29 Jun 2020 23:27:49: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:27:49: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Mon, 29 Jun 2020 23:27:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:27:49: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:28:03: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:28:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:28:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:28:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.10_summits.bed INFO @ Mon, 29 Jun 2020 23:28:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:28:26: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201886/SRX201886.20_summits.bed INFO @ Mon, 29 Jun 2020 23:28:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling