Job ID = 6454265 SRX = SRX193338 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:01:04 prefetch.2.10.7: 1) Downloading 'SRR585071'... 2020-06-21T09:01:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:09:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:09:26 prefetch.2.10.7: 1) 'SRR585071' was downloaded successfully Read 37000294 spots for SRR585071/SRR585071.sra Written 37000294 spots for SRR585071/SRR585071.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: 00:11:44 37000294 reads; of these: 37000294 (100.00%) were unpaired; of these: 1527414 (4.13%) aligned 0 times 23588221 (63.75%) aligned exactly 1 time 11884659 (32.12%) aligned >1 times 95.87% overall alignment rate Time searching: 00:11:44 Overall time: 00:11:44 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 16 files... [bam_rmdupse_core] 7947064 / 35472880 = 0.2240 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 18:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.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 18:33:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:03: 1000000 INFO @ Sun, 21 Jun 2020 18:34:10: 2000000 INFO @ Sun, 21 Jun 2020 18:34:16: 3000000 INFO @ Sun, 21 Jun 2020 18:34:22: 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 @ Sun, 21 Jun 2020 18:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.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 18:34:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:29: 5000000 INFO @ Sun, 21 Jun 2020 18:34:32: 1000000 INFO @ Sun, 21 Jun 2020 18:34:36: 6000000 INFO @ Sun, 21 Jun 2020 18:34:39: 2000000 INFO @ Sun, 21 Jun 2020 18:34:43: 7000000 INFO @ Sun, 21 Jun 2020 18:34:45: 3000000 INFO @ Sun, 21 Jun 2020 18:34:50: 8000000 INFO @ Sun, 21 Jun 2020 18:34:51: 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 @ Sun, 21 Jun 2020 18:34:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.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 18:34:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:56: 9000000 INFO @ Sun, 21 Jun 2020 18:34:58: 5000000 INFO @ Sun, 21 Jun 2020 18:35:02: 1000000 INFO @ Sun, 21 Jun 2020 18:35:03: 10000000 INFO @ Sun, 21 Jun 2020 18:35:05: 6000000 INFO @ Sun, 21 Jun 2020 18:35:08: 2000000 INFO @ Sun, 21 Jun 2020 18:35:09: 11000000 INFO @ Sun, 21 Jun 2020 18:35:12: 7000000 INFO @ Sun, 21 Jun 2020 18:35:16: 12000000 INFO @ Sun, 21 Jun 2020 18:35:16: 3000000 INFO @ Sun, 21 Jun 2020 18:35:17: 8000000 INFO @ Sun, 21 Jun 2020 18:35:23: 13000000 INFO @ Sun, 21 Jun 2020 18:35:23: 4000000 INFO @ Sun, 21 Jun 2020 18:35:24: 9000000 INFO @ Sun, 21 Jun 2020 18:35:29: 14000000 INFO @ Sun, 21 Jun 2020 18:35:29: 5000000 INFO @ Sun, 21 Jun 2020 18:35:30: 10000000 INFO @ Sun, 21 Jun 2020 18:35:36: 15000000 INFO @ Sun, 21 Jun 2020 18:35:36: 6000000 INFO @ Sun, 21 Jun 2020 18:35:37: 11000000 INFO @ Sun, 21 Jun 2020 18:35:42: 16000000 INFO @ Sun, 21 Jun 2020 18:35:43: 7000000 INFO @ Sun, 21 Jun 2020 18:35:43: 12000000 INFO @ Sun, 21 Jun 2020 18:35:49: 17000000 INFO @ Sun, 21 Jun 2020 18:35:49: 8000000 INFO @ Sun, 21 Jun 2020 18:35:50: 13000000 INFO @ Sun, 21 Jun 2020 18:35:56: 18000000 INFO @ Sun, 21 Jun 2020 18:35:56: 9000000 INFO @ Sun, 21 Jun 2020 18:35:56: 14000000 INFO @ Sun, 21 Jun 2020 18:36:02: 19000000 INFO @ Sun, 21 Jun 2020 18:36:02: 10000000 INFO @ Sun, 21 Jun 2020 18:36:03: 15000000 INFO @ Sun, 21 Jun 2020 18:36:09: 20000000 INFO @ Sun, 21 Jun 2020 18:36:09: 16000000 INFO @ Sun, 21 Jun 2020 18:36:09: 11000000 INFO @ Sun, 21 Jun 2020 18:36:16: 21000000 INFO @ Sun, 21 Jun 2020 18:36:16: 17000000 INFO @ Sun, 21 Jun 2020 18:36:16: 12000000 INFO @ Sun, 21 Jun 2020 18:36:22: 22000000 INFO @ Sun, 21 Jun 2020 18:36:22: 18000000 INFO @ Sun, 21 Jun 2020 18:36:22: 13000000 INFO @ Sun, 21 Jun 2020 18:36:29: 19000000 INFO @ Sun, 21 Jun 2020 18:36:29: 14000000 INFO @ Sun, 21 Jun 2020 18:36:29: 23000000 INFO @ Sun, 21 Jun 2020 18:36:35: 20000000 INFO @ Sun, 21 Jun 2020 18:36:35: 15000000 INFO @ Sun, 21 Jun 2020 18:36:36: 24000000 INFO @ Sun, 21 Jun 2020 18:36:42: 21000000 INFO @ Sun, 21 Jun 2020 18:36:42: 16000000 INFO @ Sun, 21 Jun 2020 18:36:43: 25000000 INFO @ Sun, 21 Jun 2020 18:36:48: 22000000 INFO @ Sun, 21 Jun 2020 18:36:49: 17000000 INFO @ Sun, 21 Jun 2020 18:36:49: 26000000 INFO @ Sun, 21 Jun 2020 18:36:55: 18000000 INFO @ Sun, 21 Jun 2020 18:36:55: 23000000 INFO @ Sun, 21 Jun 2020 18:36:56: 27000000 INFO @ Sun, 21 Jun 2020 18:37:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:37:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:37:00: #1 total tags in treatment: 27525816 INFO @ Sun, 21 Jun 2020 18:37:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:00: #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 18:37:01: #1 tags after filtering in treatment: 27525760 INFO @ Sun, 21 Jun 2020 18:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:02: 19000000 INFO @ Sun, 21 Jun 2020 18:37:02: 24000000 INFO @ Sun, 21 Jun 2020 18:37:03: #2 number of paired peaks: 746 WARNING @ Sun, 21 Jun 2020 18:37:03: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:03: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:37:03: #2 alternative fragment length(s) may be 1,52 bps INFO @ Sun, 21 Jun 2020 18:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.05_model.r WARNING @ Sun, 21 Jun 2020 18:37:03: #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 18:37:03: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Sun, 21 Jun 2020 18:37:03: #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 18:37:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:37:08: 20000000 INFO @ Sun, 21 Jun 2020 18:37:09: 25000000 INFO @ Sun, 21 Jun 2020 18:37:14: 21000000 INFO @ Sun, 21 Jun 2020 18:37:15: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:37:21: 22000000 INFO @ Sun, 21 Jun 2020 18:37:21: 27000000 INFO @ Sun, 21 Jun 2020 18:37:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:37:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:37:25: #1 total tags in treatment: 27525816 INFO @ Sun, 21 Jun 2020 18:37:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:25: #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 18:37:26: #1 tags after filtering in treatment: 27525760 INFO @ Sun, 21 Jun 2020 18:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:27: 23000000 INFO @ Sun, 21 Jun 2020 18:37:28: #2 number of paired peaks: 746 WARNING @ Sun, 21 Jun 2020 18:37:28: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:28: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:37:28: #2 alternative fragment length(s) may be 1,52 bps INFO @ Sun, 21 Jun 2020 18:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.10_model.r WARNING @ Sun, 21 Jun 2020 18:37:28: #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 18:37:28: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Sun, 21 Jun 2020 18:37:28: #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 18:37:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:37:34: 24000000 INFO @ Sun, 21 Jun 2020 18:37:39: 25000000 INFO @ Sun, 21 Jun 2020 18:37:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:45: 26000000 INFO @ Sun, 21 Jun 2020 18:37:51: 27000000 INFO @ Sun, 21 Jun 2020 18:37:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:37:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:37:55: #1 total tags in treatment: 27525816 INFO @ Sun, 21 Jun 2020 18:37:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:55: #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 18:37:56: #1 tags after filtering in treatment: 27525760 INFO @ Sun, 21 Jun 2020 18:37:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:58: #2 number of paired peaks: 746 WARNING @ Sun, 21 Jun 2020 18:37:58: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:58: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:37:58: #2 alternative fragment length(s) may be 1,52 bps INFO @ Sun, 21 Jun 2020 18:37:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.20_model.r WARNING @ Sun, 21 Jun 2020 18:37:58: #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 18:37:58: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Sun, 21 Jun 2020 18:37:58: #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 18:37:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:37:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.05_summits.bed INFO @ Sun, 21 Jun 2020 18:37:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:38:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:38:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.10_summits.bed INFO @ Sun, 21 Jun 2020 18:38:24: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:38:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:38:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193338/SRX193338.20_summits.bed INFO @ Sun, 21 Jun 2020 18:38:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling