Job ID = 6527801 SRX = SRX287673 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:34:36 prefetch.2.10.7: 1) Downloading 'SRR869861'... 2020-06-29T13:34:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:39:06 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:39:06 prefetch.2.10.7: 1) 'SRR869861' was downloaded successfully Read 26924228 spots for SRR869861/SRR869861.sra Written 26924228 spots for SRR869861/SRR869861.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: 00:11:03 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1125826 (4.18%) aligned 0 times 17097138 (63.50%) aligned exactly 1 time 8701264 (32.32%) aligned >1 times 95.82% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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 12 files... [bam_rmdupse_core] 3992042 / 25798402 = 0.1547 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 23:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.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 23:03:17: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:03:17: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:03:23: 1000000 INFO @ Mon, 29 Jun 2020 23:03:29: 2000000 INFO @ Mon, 29 Jun 2020 23:03:34: 3000000 INFO @ Mon, 29 Jun 2020 23:03:40: 4000000 INFO @ Mon, 29 Jun 2020 23:03:45: 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 @ Mon, 29 Jun 2020 23:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.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 23:03:47: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:03:47: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:03:51: 6000000 INFO @ Mon, 29 Jun 2020 23:03:53: 1000000 INFO @ Mon, 29 Jun 2020 23:03:57: 7000000 INFO @ Mon, 29 Jun 2020 23:03:59: 2000000 INFO @ Mon, 29 Jun 2020 23:04:03: 8000000 INFO @ Mon, 29 Jun 2020 23:04:05: 3000000 INFO @ Mon, 29 Jun 2020 23:04:09: 9000000 INFO @ Mon, 29 Jun 2020 23:04:11: 4000000 INFO @ Mon, 29 Jun 2020 23:04:15: 10000000 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 23:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.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 23:04:17: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:04:17: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:04:17: 5000000 INFO @ Mon, 29 Jun 2020 23:04:21: 11000000 INFO @ Mon, 29 Jun 2020 23:04:24: 6000000 INFO @ Mon, 29 Jun 2020 23:04:24: 1000000 INFO @ Mon, 29 Jun 2020 23:04:27: 12000000 INFO @ Mon, 29 Jun 2020 23:04:30: 7000000 INFO @ Mon, 29 Jun 2020 23:04:30: 2000000 INFO @ Mon, 29 Jun 2020 23:04:33: 13000000 INFO @ Mon, 29 Jun 2020 23:04:36: 8000000 INFO @ Mon, 29 Jun 2020 23:04:36: 3000000 INFO @ Mon, 29 Jun 2020 23:04:39: 14000000 INFO @ Mon, 29 Jun 2020 23:04:42: 9000000 INFO @ Mon, 29 Jun 2020 23:04:42: 4000000 INFO @ Mon, 29 Jun 2020 23:04:45: 15000000 INFO @ Mon, 29 Jun 2020 23:04:48: 10000000 INFO @ Mon, 29 Jun 2020 23:04:48: 5000000 INFO @ Mon, 29 Jun 2020 23:04:51: 16000000 INFO @ Mon, 29 Jun 2020 23:04:54: 11000000 INFO @ Mon, 29 Jun 2020 23:04:54: 6000000 INFO @ Mon, 29 Jun 2020 23:04:57: 17000000 INFO @ Mon, 29 Jun 2020 23:05:00: 12000000 INFO @ Mon, 29 Jun 2020 23:05:00: 7000000 INFO @ Mon, 29 Jun 2020 23:05:03: 18000000 INFO @ Mon, 29 Jun 2020 23:05:06: 13000000 INFO @ Mon, 29 Jun 2020 23:05:07: 8000000 INFO @ Mon, 29 Jun 2020 23:05:09: 19000000 INFO @ Mon, 29 Jun 2020 23:05:12: 14000000 INFO @ Mon, 29 Jun 2020 23:05:13: 9000000 INFO @ Mon, 29 Jun 2020 23:05:15: 20000000 INFO @ Mon, 29 Jun 2020 23:05:18: 15000000 INFO @ Mon, 29 Jun 2020 23:05:19: 10000000 INFO @ Mon, 29 Jun 2020 23:05:21: 21000000 INFO @ Mon, 29 Jun 2020 23:05:24: 16000000 INFO @ Mon, 29 Jun 2020 23:05:25: 11000000 INFO @ Mon, 29 Jun 2020 23:05:26: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:05:26: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:05:26: #1 total tags in treatment: 21806360 INFO @ Mon, 29 Jun 2020 23:05:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:05:26: #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 23:05:26: #1 tags after filtering in treatment: 21806360 INFO @ Mon, 29 Jun 2020 23:05:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:05:26: #1 finished! INFO @ Mon, 29 Jun 2020 23:05:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:05:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:05:28: #2 number of paired peaks: 160 WARNING @ Mon, 29 Jun 2020 23:05:28: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 29 Jun 2020 23:05:28: start model_add_line... INFO @ Mon, 29 Jun 2020 23:05:28: start X-correlation... INFO @ Mon, 29 Jun 2020 23:05:28: end of X-cor INFO @ Mon, 29 Jun 2020 23:05:28: #2 finished! INFO @ Mon, 29 Jun 2020 23:05:28: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:05:28: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:05:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.05_model.r WARNING @ Mon, 29 Jun 2020 23:05:28: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:05:28: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:05:28: #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 23:05:28: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:05:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:05:30: 17000000 INFO @ Mon, 29 Jun 2020 23:05:31: 12000000 INFO @ Mon, 29 Jun 2020 23:05:36: 18000000 INFO @ Mon, 29 Jun 2020 23:05:36: 13000000 INFO @ Mon, 29 Jun 2020 23:05:42: 19000000 INFO @ Mon, 29 Jun 2020 23:05:42: 14000000 INFO @ Mon, 29 Jun 2020 23:05:47: 20000000 INFO @ Mon, 29 Jun 2020 23:05:48: 15000000 INFO @ Mon, 29 Jun 2020 23:05:53: 21000000 INFO @ Mon, 29 Jun 2020 23:05:54: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:05:58: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:05:58: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:05:58: #1 total tags in treatment: 21806360 INFO @ Mon, 29 Jun 2020 23:05:58: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:05:58: #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 23:05:58: #1 tags after filtering in treatment: 21806360 INFO @ Mon, 29 Jun 2020 23:05:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:05:58: #1 finished! INFO @ Mon, 29 Jun 2020 23:05:58: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:05:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:06:00: #2 number of paired peaks: 160 WARNING @ Mon, 29 Jun 2020 23:06:00: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 29 Jun 2020 23:06:00: start model_add_line... INFO @ Mon, 29 Jun 2020 23:06:00: start X-correlation... INFO @ Mon, 29 Jun 2020 23:06:00: end of X-cor INFO @ Mon, 29 Jun 2020 23:06:00: #2 finished! INFO @ Mon, 29 Jun 2020 23:06:00: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:06:00: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:06:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.10_model.r WARNING @ Mon, 29 Jun 2020 23:06:00: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:06:00: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:06:00: #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 23:06:00: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:06:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:06:00: 17000000 INFO @ Mon, 29 Jun 2020 23:06:05: 18000000 INFO @ Mon, 29 Jun 2020 23:06:06: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:06:11: 19000000 INFO @ Mon, 29 Jun 2020 23:06:16: 20000000 INFO @ Mon, 29 Jun 2020 23:06:22: 21000000 INFO @ Mon, 29 Jun 2020 23:06:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:06:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:06:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.05_summits.bed INFO @ Mon, 29 Jun 2020 23:06:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2231 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:06:26: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:06:26: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:06:26: #1 total tags in treatment: 21806360 INFO @ Mon, 29 Jun 2020 23:06:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:06:26: #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 23:06:27: #1 tags after filtering in treatment: 21806360 INFO @ Mon, 29 Jun 2020 23:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:06:27: #1 finished! INFO @ Mon, 29 Jun 2020 23:06:27: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:06:28: #2 number of paired peaks: 160 WARNING @ Mon, 29 Jun 2020 23:06:28: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 29 Jun 2020 23:06:28: start model_add_line... INFO @ Mon, 29 Jun 2020 23:06:28: start X-correlation... INFO @ Mon, 29 Jun 2020 23:06:28: end of X-cor INFO @ Mon, 29 Jun 2020 23:06:28: #2 finished! INFO @ Mon, 29 Jun 2020 23:06:28: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:06:28: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.20_model.r WARNING @ Mon, 29 Jun 2020 23:06:28: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:06:28: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:06:28: #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 23:06:28: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:06:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:06:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:06:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:06:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.10_summits.bed INFO @ Mon, 29 Jun 2020 23:06:57: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1879 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:07:07: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:07:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:07:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:07:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287673/SRX287673.20_summits.bed INFO @ Mon, 29 Jun 2020 23:07:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1453 records, 4 fields): 2 millis CompletedMACS2peakCalling