Job ID = 6527488 SRX = SRX032113 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:52:53 prefetch.2.10.7: 1) Downloading 'SRR073931'... 2020-06-29T12:52:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:54:30 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:54:31 prefetch.2.10.7: 'SRR073931' is valid 2020-06-29T12:54:31 prefetch.2.10.7: 1) 'SRR073931' was downloaded successfully Read 13464307 spots for SRR073931/SRR073931.sra Written 13464307 spots for SRR073931/SRR073931.sra 2020-06-29T12:55:19 prefetch.2.10.7: 1) Downloading 'SRR073932'... 2020-06-29T12:55:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:57:21 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:57:22 prefetch.2.10.7: 'SRR073932' is valid 2020-06-29T12:57:22 prefetch.2.10.7: 1) 'SRR073932' was downloaded successfully Read 23880214 spots for SRR073932/SRR073932.sra Written 23880214 spots for SRR073932/SRR073932.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: 00:15:04 37344521 reads; of these: 37344521 (100.00%) were unpaired; of these: 722057 (1.93%) aligned 0 times 20116910 (53.87%) aligned exactly 1 time 16505554 (44.20%) aligned >1 times 98.07% overall alignment rate Time searching: 00:15:04 Overall time: 00:15:04 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] 11994248 / 36622464 = 0.3275 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 22:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.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 22:28:23: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:28:23: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:28:30: 1000000 INFO @ Mon, 29 Jun 2020 22:28:36: 2000000 INFO @ Mon, 29 Jun 2020 22:28:42: 3000000 INFO @ Mon, 29 Jun 2020 22:28:49: 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 22:28:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.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 22:28:53: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:28:53: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:28:55: 5000000 INFO @ Mon, 29 Jun 2020 22:28:59: 1000000 INFO @ Mon, 29 Jun 2020 22:29:02: 6000000 INFO @ Mon, 29 Jun 2020 22:29:05: 2000000 INFO @ Mon, 29 Jun 2020 22:29:08: 7000000 INFO @ Mon, 29 Jun 2020 22:29:11: 3000000 INFO @ Mon, 29 Jun 2020 22:29:15: 8000000 INFO @ Mon, 29 Jun 2020 22:29:17: 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 22:29:21: 9000000 INFO @ Mon, 29 Jun 2020 22:29:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.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 22:29:23: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:29:23: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:29:23: 5000000 INFO @ Mon, 29 Jun 2020 22:29:28: 10000000 INFO @ Mon, 29 Jun 2020 22:29:29: 1000000 INFO @ Mon, 29 Jun 2020 22:29:29: 6000000 INFO @ Mon, 29 Jun 2020 22:29:35: 11000000 INFO @ Mon, 29 Jun 2020 22:29:35: 7000000 INFO @ Mon, 29 Jun 2020 22:29:35: 2000000 INFO @ Mon, 29 Jun 2020 22:29:41: 8000000 INFO @ Mon, 29 Jun 2020 22:29:42: 12000000 INFO @ Mon, 29 Jun 2020 22:29:42: 3000000 INFO @ Mon, 29 Jun 2020 22:29:48: 9000000 INFO @ Mon, 29 Jun 2020 22:29:48: 4000000 INFO @ Mon, 29 Jun 2020 22:29:48: 13000000 INFO @ Mon, 29 Jun 2020 22:29:54: 10000000 INFO @ Mon, 29 Jun 2020 22:29:55: 5000000 INFO @ Mon, 29 Jun 2020 22:29:55: 14000000 INFO @ Mon, 29 Jun 2020 22:30:00: 11000000 INFO @ Mon, 29 Jun 2020 22:30:01: 6000000 INFO @ Mon, 29 Jun 2020 22:30:02: 15000000 INFO @ Mon, 29 Jun 2020 22:30:07: 12000000 INFO @ Mon, 29 Jun 2020 22:30:07: 7000000 INFO @ Mon, 29 Jun 2020 22:30:08: 16000000 INFO @ Mon, 29 Jun 2020 22:30:13: 13000000 INFO @ Mon, 29 Jun 2020 22:30:14: 8000000 INFO @ Mon, 29 Jun 2020 22:30:15: 17000000 INFO @ Mon, 29 Jun 2020 22:30:19: 14000000 INFO @ Mon, 29 Jun 2020 22:30:20: 9000000 INFO @ Mon, 29 Jun 2020 22:30:22: 18000000 INFO @ Mon, 29 Jun 2020 22:30:25: 15000000 INFO @ Mon, 29 Jun 2020 22:30:26: 10000000 INFO @ Mon, 29 Jun 2020 22:30:28: 19000000 INFO @ Mon, 29 Jun 2020 22:30:32: 16000000 INFO @ Mon, 29 Jun 2020 22:30:33: 11000000 INFO @ Mon, 29 Jun 2020 22:30:35: 20000000 INFO @ Mon, 29 Jun 2020 22:30:38: 17000000 INFO @ Mon, 29 Jun 2020 22:30:39: 12000000 INFO @ Mon, 29 Jun 2020 22:30:42: 21000000 INFO @ Mon, 29 Jun 2020 22:30:44: 18000000 INFO @ Mon, 29 Jun 2020 22:30:46: 13000000 INFO @ Mon, 29 Jun 2020 22:30:49: 22000000 INFO @ Mon, 29 Jun 2020 22:30:50: 19000000 INFO @ Mon, 29 Jun 2020 22:30:53: 14000000 INFO @ Mon, 29 Jun 2020 22:30:56: 23000000 INFO @ Mon, 29 Jun 2020 22:30:57: 20000000 INFO @ Mon, 29 Jun 2020 22:30:59: 15000000 INFO @ Mon, 29 Jun 2020 22:31:02: 24000000 INFO @ Mon, 29 Jun 2020 22:31:03: 21000000 INFO @ Mon, 29 Jun 2020 22:31:06: 16000000 INFO @ Mon, 29 Jun 2020 22:31:07: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:31:07: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:31:07: #1 total tags in treatment: 24628216 INFO @ Mon, 29 Jun 2020 22:31:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:31:07: #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 22:31:07: #1 tags after filtering in treatment: 24628216 INFO @ Mon, 29 Jun 2020 22:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:31:07: #1 finished! INFO @ Mon, 29 Jun 2020 22:31:07: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:31:09: #2 number of paired peaks: 168 WARNING @ Mon, 29 Jun 2020 22:31:09: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Mon, 29 Jun 2020 22:31:09: start model_add_line... INFO @ Mon, 29 Jun 2020 22:31:09: start X-correlation... INFO @ Mon, 29 Jun 2020 22:31:09: end of X-cor INFO @ Mon, 29 Jun 2020 22:31:09: #2 finished! INFO @ Mon, 29 Jun 2020 22:31:09: #2 predicted fragment length is 39 bps INFO @ Mon, 29 Jun 2020 22:31:09: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 29 Jun 2020 22:31:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.05_model.r WARNING @ Mon, 29 Jun 2020 22:31:09: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:31:09: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 29 Jun 2020 22:31:09: #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 22:31:09: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:31:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:31:09: 22000000 INFO @ Mon, 29 Jun 2020 22:31:12: 17000000 INFO @ Mon, 29 Jun 2020 22:31:15: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:31:19: 18000000 INFO @ Mon, 29 Jun 2020 22:31:21: 24000000 INFO @ Mon, 29 Jun 2020 22:31:25: 19000000 INFO @ Mon, 29 Jun 2020 22:31:25: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:31:25: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:31:25: #1 total tags in treatment: 24628216 INFO @ Mon, 29 Jun 2020 22:31:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:31:25: #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 22:31:26: #1 tags after filtering in treatment: 24628216 INFO @ Mon, 29 Jun 2020 22:31:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:31:26: #1 finished! INFO @ Mon, 29 Jun 2020 22:31:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:31:27: #2 number of paired peaks: 168 WARNING @ Mon, 29 Jun 2020 22:31:27: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Mon, 29 Jun 2020 22:31:27: start model_add_line... INFO @ Mon, 29 Jun 2020 22:31:27: start X-correlation... INFO @ Mon, 29 Jun 2020 22:31:27: end of X-cor INFO @ Mon, 29 Jun 2020 22:31:27: #2 finished! INFO @ Mon, 29 Jun 2020 22:31:27: #2 predicted fragment length is 39 bps INFO @ Mon, 29 Jun 2020 22:31:27: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 29 Jun 2020 22:31:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.10_model.r WARNING @ Mon, 29 Jun 2020 22:31:27: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:31:27: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 29 Jun 2020 22:31:27: #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 22:31:27: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:31:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:31:31: 20000000 INFO @ Mon, 29 Jun 2020 22:31:36: 21000000 INFO @ Mon, 29 Jun 2020 22:31:42: 22000000 INFO @ Mon, 29 Jun 2020 22:31:47: 23000000 INFO @ Mon, 29 Jun 2020 22:31:52: 24000000 INFO @ Mon, 29 Jun 2020 22:31:54: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:31:56: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:31:56: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:31:56: #1 total tags in treatment: 24628216 INFO @ Mon, 29 Jun 2020 22:31:56: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:31:56: #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 22:31:56: #1 tags after filtering in treatment: 24628216 INFO @ Mon, 29 Jun 2020 22:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:31:56: #1 finished! INFO @ Mon, 29 Jun 2020 22:31:56: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:31:58: #2 number of paired peaks: 168 WARNING @ Mon, 29 Jun 2020 22:31:58: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Mon, 29 Jun 2020 22:31:58: start model_add_line... INFO @ Mon, 29 Jun 2020 22:31:58: start X-correlation... INFO @ Mon, 29 Jun 2020 22:31:58: end of X-cor INFO @ Mon, 29 Jun 2020 22:31:58: #2 finished! INFO @ Mon, 29 Jun 2020 22:31:58: #2 predicted fragment length is 39 bps INFO @ Mon, 29 Jun 2020 22:31:58: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 29 Jun 2020 22:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.20_model.r WARNING @ Mon, 29 Jun 2020 22:31:58: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:31:58: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 29 Jun 2020 22:31:58: #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 22:31:58: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:31:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:32:14: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:32:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:32:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:32:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.05_summits.bed INFO @ Mon, 29 Jun 2020 22:32:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3371 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.10_summits.bed INFO @ Mon, 29 Jun 2020 22:32:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1948 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:32:48: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:33:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:33:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:33:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032113/SRX032113.20_summits.bed INFO @ Mon, 29 Jun 2020 22:33:14: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1152 records, 4 fields): 3 millis CompletedMACS2peakCalling