Job ID = 6527628 SRX = SRX159171 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:35:10 prefetch.2.10.7: 1) Downloading 'SRR520452'... 2020-06-29T13:35:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:37:11 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:37:11 prefetch.2.10.7: 1) 'SRR520452' was downloaded successfully Read 29495696 spots for SRR520452/SRR520452.sra Written 29495696 spots for SRR520452/SRR520452.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: 00:08:07 29495696 reads; of these: 29495696 (100.00%) were unpaired; of these: 2982898 (10.11%) aligned 0 times 17984627 (60.97%) aligned exactly 1 time 8528171 (28.91%) aligned >1 times 89.89% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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 8 files... [bam_rmdupse_core] 3048454 / 26512798 = 0.1150 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 22:56:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.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 22:56:52: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:56:52: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:56:57: 1000000 INFO @ Mon, 29 Jun 2020 22:57:01: 2000000 INFO @ Mon, 29 Jun 2020 22:57:05: 3000000 INFO @ Mon, 29 Jun 2020 22:57:10: 4000000 INFO @ Mon, 29 Jun 2020 22:57:14: 5000000 INFO @ Mon, 29 Jun 2020 22:57:18: 6000000 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 22:57:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.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 22:57:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:57:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:57:22: 7000000 INFO @ Mon, 29 Jun 2020 22:57:27: 1000000 INFO @ Mon, 29 Jun 2020 22:57:27: 8000000 INFO @ Mon, 29 Jun 2020 22:57:31: 2000000 INFO @ Mon, 29 Jun 2020 22:57:31: 9000000 INFO @ Mon, 29 Jun 2020 22:57:35: 3000000 INFO @ Mon, 29 Jun 2020 22:57:35: 10000000 INFO @ Mon, 29 Jun 2020 22:57:40: 4000000 INFO @ Mon, 29 Jun 2020 22:57:40: 11000000 INFO @ Mon, 29 Jun 2020 22:57:44: 5000000 INFO @ Mon, 29 Jun 2020 22:57:44: 12000000 INFO @ Mon, 29 Jun 2020 22:57:48: 6000000 INFO @ Mon, 29 Jun 2020 22:57:48: 13000000 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 22:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.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 22:57:52: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:57:52: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:57:53: 14000000 INFO @ Mon, 29 Jun 2020 22:57:53: 7000000 INFO @ Mon, 29 Jun 2020 22:57:57: 1000000 INFO @ Mon, 29 Jun 2020 22:57:57: 15000000 INFO @ Mon, 29 Jun 2020 22:57:57: 8000000 INFO @ Mon, 29 Jun 2020 22:58:01: 2000000 INFO @ Mon, 29 Jun 2020 22:58:02: 16000000 INFO @ Mon, 29 Jun 2020 22:58:02: 9000000 INFO @ Mon, 29 Jun 2020 22:58:05: 3000000 INFO @ Mon, 29 Jun 2020 22:58:06: 17000000 INFO @ Mon, 29 Jun 2020 22:58:06: 10000000 INFO @ Mon, 29 Jun 2020 22:58:10: 4000000 INFO @ Mon, 29 Jun 2020 22:58:10: 18000000 INFO @ Mon, 29 Jun 2020 22:58:10: 11000000 INFO @ Mon, 29 Jun 2020 22:58:14: 5000000 INFO @ Mon, 29 Jun 2020 22:58:15: 19000000 INFO @ Mon, 29 Jun 2020 22:58:15: 12000000 INFO @ Mon, 29 Jun 2020 22:58:18: 6000000 INFO @ Mon, 29 Jun 2020 22:58:19: 13000000 INFO @ Mon, 29 Jun 2020 22:58:19: 20000000 INFO @ Mon, 29 Jun 2020 22:58:23: 7000000 INFO @ Mon, 29 Jun 2020 22:58:23: 14000000 INFO @ Mon, 29 Jun 2020 22:58:24: 21000000 INFO @ Mon, 29 Jun 2020 22:58:27: 8000000 INFO @ Mon, 29 Jun 2020 22:58:28: 15000000 INFO @ Mon, 29 Jun 2020 22:58:28: 22000000 INFO @ Mon, 29 Jun 2020 22:58:31: 9000000 INFO @ Mon, 29 Jun 2020 22:58:32: 16000000 INFO @ Mon, 29 Jun 2020 22:58:33: 23000000 INFO @ Mon, 29 Jun 2020 22:58:35: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:58:35: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:58:35: #1 total tags in treatment: 23464344 INFO @ Mon, 29 Jun 2020 22:58:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:58:35: #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 22:58:35: #1 tags after filtering in treatment: 23464344 INFO @ Mon, 29 Jun 2020 22:58:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:58:35: #1 finished! INFO @ Mon, 29 Jun 2020 22:58:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:58:36: 10000000 INFO @ Mon, 29 Jun 2020 22:58:37: 17000000 INFO @ Mon, 29 Jun 2020 22:58:37: #2 number of paired peaks: 387 WARNING @ Mon, 29 Jun 2020 22:58:37: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Mon, 29 Jun 2020 22:58:37: start model_add_line... INFO @ Mon, 29 Jun 2020 22:58:37: start X-correlation... INFO @ Mon, 29 Jun 2020 22:58:37: end of X-cor INFO @ Mon, 29 Jun 2020 22:58:37: #2 finished! INFO @ Mon, 29 Jun 2020 22:58:37: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:58:37: #2 alternative fragment length(s) may be 2,23,581 bps INFO @ Mon, 29 Jun 2020 22:58:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.05_model.r WARNING @ Mon, 29 Jun 2020 22:58:37: #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 22:58:37: #2 You may need to consider one of the other alternative d(s): 2,23,581 WARNING @ Mon, 29 Jun 2020 22:58:37: #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 22:58:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:58:40: 11000000 INFO @ Mon, 29 Jun 2020 22:58:41: 18000000 INFO @ Mon, 29 Jun 2020 22:58:44: 12000000 INFO @ Mon, 29 Jun 2020 22:58:45: 19000000 INFO @ Mon, 29 Jun 2020 22:58:49: 13000000 INFO @ Mon, 29 Jun 2020 22:58:50: 20000000 INFO @ Mon, 29 Jun 2020 22:58:53: 14000000 INFO @ Mon, 29 Jun 2020 22:58:54: 21000000 INFO @ Mon, 29 Jun 2020 22:58:57: 15000000 INFO @ Mon, 29 Jun 2020 22:58:58: 22000000 INFO @ Mon, 29 Jun 2020 22:59:02: 16000000 INFO @ Mon, 29 Jun 2020 22:59:03: 23000000 INFO @ Mon, 29 Jun 2020 22:59:05: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:59:05: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:59:05: #1 total tags in treatment: 23464344 INFO @ Mon, 29 Jun 2020 22:59:05: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:05: #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 22:59:05: #1 tags after filtering in treatment: 23464344 INFO @ Mon, 29 Jun 2020 22:59:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:05: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:05: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:06: 17000000 INFO @ Mon, 29 Jun 2020 22:59:07: #2 number of paired peaks: 387 WARNING @ Mon, 29 Jun 2020 22:59:07: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Mon, 29 Jun 2020 22:59:07: start model_add_line... INFO @ Mon, 29 Jun 2020 22:59:07: start X-correlation... INFO @ Mon, 29 Jun 2020 22:59:07: end of X-cor INFO @ Mon, 29 Jun 2020 22:59:07: #2 finished! INFO @ Mon, 29 Jun 2020 22:59:07: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:59:07: #2 alternative fragment length(s) may be 2,23,581 bps INFO @ Mon, 29 Jun 2020 22:59:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.10_model.r WARNING @ Mon, 29 Jun 2020 22:59:07: #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 22:59:07: #2 You may need to consider one of the other alternative d(s): 2,23,581 WARNING @ Mon, 29 Jun 2020 22:59:07: #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 22:59:07: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:59:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:59:10: 18000000 INFO @ Mon, 29 Jun 2020 22:59:14: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:59:14: 19000000 INFO @ Mon, 29 Jun 2020 22:59:19: 20000000 INFO @ Mon, 29 Jun 2020 22:59:23: 21000000 INFO @ Mon, 29 Jun 2020 22:59:27: 22000000 INFO @ Mon, 29 Jun 2020 22:59:32: 23000000 INFO @ Mon, 29 Jun 2020 22:59:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:59:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:59:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.05_summits.bed INFO @ Mon, 29 Jun 2020 22:59:33: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:59:34: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:59:34: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:59:34: #1 total tags in treatment: 23464344 INFO @ Mon, 29 Jun 2020 22:59:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:34: #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 22:59:34: #1 tags after filtering in treatment: 23464344 INFO @ Mon, 29 Jun 2020 22:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:34: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:36: #2 number of paired peaks: 387 WARNING @ Mon, 29 Jun 2020 22:59:36: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Mon, 29 Jun 2020 22:59:36: start model_add_line... INFO @ Mon, 29 Jun 2020 22:59:36: start X-correlation... INFO @ Mon, 29 Jun 2020 22:59:36: end of X-cor INFO @ Mon, 29 Jun 2020 22:59:36: #2 finished! INFO @ Mon, 29 Jun 2020 22:59:36: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 22:59:36: #2 alternative fragment length(s) may be 2,23,581 bps INFO @ Mon, 29 Jun 2020 22:59:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.20_model.r WARNING @ Mon, 29 Jun 2020 22:59:36: #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 22:59:36: #2 You may need to consider one of the other alternative d(s): 2,23,581 WARNING @ Mon, 29 Jun 2020 22:59:36: #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 22:59:36: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:59:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:59:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.10_summits.bed INFO @ Mon, 29 Jun 2020 23:00:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:00:13: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159171/SRX159171.20_summits.bed INFO @ Mon, 29 Jun 2020 23:00:32: 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。