Job ID = 6498675 SRX = SRX685467 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:50:48 prefetch.2.10.7: 1) Downloading 'SRR1556389'... 2020-06-25T23:50:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:55:13 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:55:13 prefetch.2.10.7: 1) 'SRR1556389' was downloaded successfully Read 45595988 spots for SRR1556389/SRR1556389.sra Written 45595988 spots for SRR1556389/SRR1556389.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: 00:18:46 45595988 reads; of these: 45595988 (100.00%) were unpaired; of these: 1226059 (2.69%) aligned 0 times 26949628 (59.11%) aligned exactly 1 time 17420301 (38.21%) aligned >1 times 97.31% overall alignment rate Time searching: 00:18:46 Overall time: 00:18:46 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 20 files... [bam_rmdupse_core] 10137754 / 44369929 = 0.2285 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 @ Fri, 26 Jun 2020 09:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.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 @ Fri, 26 Jun 2020 09:26:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:16: 1000000 INFO @ Fri, 26 Jun 2020 09:26:22: 2000000 INFO @ Fri, 26 Jun 2020 09:26:28: 3000000 INFO @ Fri, 26 Jun 2020 09:26:33: 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 @ Fri, 26 Jun 2020 09:26:39: 5000000 INFO @ Fri, 26 Jun 2020 09:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.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 @ Fri, 26 Jun 2020 09:26:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:45: 6000000 INFO @ Fri, 26 Jun 2020 09:26:47: 1000000 INFO @ Fri, 26 Jun 2020 09:26:52: 7000000 INFO @ Fri, 26 Jun 2020 09:26:53: 2000000 INFO @ Fri, 26 Jun 2020 09:26:58: 8000000 INFO @ Fri, 26 Jun 2020 09:27:00: 3000000 INFO @ Fri, 26 Jun 2020 09:27:05: 9000000 INFO @ Fri, 26 Jun 2020 09:27:07: 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 @ Fri, 26 Jun 2020 09:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.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 @ Fri, 26 Jun 2020 09:27:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:27:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:27:11: 10000000 INFO @ Fri, 26 Jun 2020 09:27:13: 5000000 INFO @ Fri, 26 Jun 2020 09:27:17: 1000000 INFO @ Fri, 26 Jun 2020 09:27:18: 11000000 INFO @ Fri, 26 Jun 2020 09:27:20: 6000000 INFO @ Fri, 26 Jun 2020 09:27:24: 2000000 INFO @ Fri, 26 Jun 2020 09:27:24: 12000000 INFO @ Fri, 26 Jun 2020 09:27:27: 7000000 INFO @ Fri, 26 Jun 2020 09:27:30: 3000000 INFO @ Fri, 26 Jun 2020 09:27:31: 13000000 INFO @ Fri, 26 Jun 2020 09:27:33: 8000000 INFO @ Fri, 26 Jun 2020 09:27:37: 4000000 INFO @ Fri, 26 Jun 2020 09:27:37: 14000000 INFO @ Fri, 26 Jun 2020 09:27:40: 9000000 INFO @ Fri, 26 Jun 2020 09:27:44: 5000000 INFO @ Fri, 26 Jun 2020 09:27:44: 15000000 INFO @ Fri, 26 Jun 2020 09:27:47: 10000000 INFO @ Fri, 26 Jun 2020 09:27:50: 6000000 INFO @ Fri, 26 Jun 2020 09:27:50: 16000000 INFO @ Fri, 26 Jun 2020 09:27:54: 11000000 INFO @ Fri, 26 Jun 2020 09:27:57: 7000000 INFO @ Fri, 26 Jun 2020 09:27:57: 17000000 INFO @ Fri, 26 Jun 2020 09:28:00: 12000000 INFO @ Fri, 26 Jun 2020 09:28:03: 8000000 INFO @ Fri, 26 Jun 2020 09:28:04: 18000000 INFO @ Fri, 26 Jun 2020 09:28:07: 13000000 INFO @ Fri, 26 Jun 2020 09:28:10: 19000000 INFO @ Fri, 26 Jun 2020 09:28:10: 9000000 INFO @ Fri, 26 Jun 2020 09:28:14: 14000000 INFO @ Fri, 26 Jun 2020 09:28:17: 20000000 INFO @ Fri, 26 Jun 2020 09:28:17: 10000000 INFO @ Fri, 26 Jun 2020 09:28:20: 15000000 INFO @ Fri, 26 Jun 2020 09:28:23: 21000000 INFO @ Fri, 26 Jun 2020 09:28:23: 11000000 INFO @ Fri, 26 Jun 2020 09:28:27: 16000000 INFO @ Fri, 26 Jun 2020 09:28:30: 22000000 INFO @ Fri, 26 Jun 2020 09:28:30: 12000000 INFO @ Fri, 26 Jun 2020 09:28:34: 17000000 INFO @ Fri, 26 Jun 2020 09:28:36: 23000000 INFO @ Fri, 26 Jun 2020 09:28:37: 13000000 INFO @ Fri, 26 Jun 2020 09:28:41: 18000000 INFO @ Fri, 26 Jun 2020 09:28:43: 24000000 INFO @ Fri, 26 Jun 2020 09:28:43: 14000000 INFO @ Fri, 26 Jun 2020 09:28:47: 19000000 INFO @ Fri, 26 Jun 2020 09:28:49: 25000000 INFO @ Fri, 26 Jun 2020 09:28:50: 15000000 INFO @ Fri, 26 Jun 2020 09:28:54: 20000000 INFO @ Fri, 26 Jun 2020 09:28:56: 26000000 INFO @ Fri, 26 Jun 2020 09:28:57: 16000000 INFO @ Fri, 26 Jun 2020 09:29:01: 21000000 INFO @ Fri, 26 Jun 2020 09:29:02: 27000000 INFO @ Fri, 26 Jun 2020 09:29:03: 17000000 INFO @ Fri, 26 Jun 2020 09:29:07: 22000000 INFO @ Fri, 26 Jun 2020 09:29:09: 28000000 INFO @ Fri, 26 Jun 2020 09:29:10: 18000000 INFO @ Fri, 26 Jun 2020 09:29:14: 23000000 INFO @ Fri, 26 Jun 2020 09:29:15: 29000000 INFO @ Fri, 26 Jun 2020 09:29:17: 19000000 INFO @ Fri, 26 Jun 2020 09:29:21: 24000000 INFO @ Fri, 26 Jun 2020 09:29:22: 30000000 INFO @ Fri, 26 Jun 2020 09:29:23: 20000000 INFO @ Fri, 26 Jun 2020 09:29:27: 25000000 INFO @ Fri, 26 Jun 2020 09:29:28: 31000000 INFO @ Fri, 26 Jun 2020 09:29:30: 21000000 INFO @ Fri, 26 Jun 2020 09:29:34: 26000000 INFO @ Fri, 26 Jun 2020 09:29:35: 32000000 INFO @ Fri, 26 Jun 2020 09:29:36: 22000000 INFO @ Fri, 26 Jun 2020 09:29:41: 27000000 INFO @ Fri, 26 Jun 2020 09:29:42: 33000000 INFO @ Fri, 26 Jun 2020 09:29:43: 23000000 INFO @ Fri, 26 Jun 2020 09:29:47: 28000000 INFO @ Fri, 26 Jun 2020 09:29:48: 34000000 INFO @ Fri, 26 Jun 2020 09:29:50: 24000000 INFO @ Fri, 26 Jun 2020 09:29:50: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:29:50: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:29:50: #1 total tags in treatment: 34232175 INFO @ Fri, 26 Jun 2020 09:29:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:29:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:29:50: #1 tags after filtering in treatment: 34232175 INFO @ Fri, 26 Jun 2020 09:29:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:29:50: #1 finished! INFO @ Fri, 26 Jun 2020 09:29:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:29:53: #2 number of paired peaks: 212 WARNING @ Fri, 26 Jun 2020 09:29:53: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Fri, 26 Jun 2020 09:29:53: start model_add_line... INFO @ Fri, 26 Jun 2020 09:29:53: start X-correlation... INFO @ Fri, 26 Jun 2020 09:29:53: end of X-cor INFO @ Fri, 26 Jun 2020 09:29:53: #2 finished! INFO @ Fri, 26 Jun 2020 09:29:53: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 09:29:53: #2 alternative fragment length(s) may be 1,50,114,127,566 bps INFO @ Fri, 26 Jun 2020 09:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.05_model.r WARNING @ Fri, 26 Jun 2020 09:29:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:29:53: #2 You may need to consider one of the other alternative d(s): 1,50,114,127,566 WARNING @ Fri, 26 Jun 2020 09:29:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:29:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:29:54: 29000000 INFO @ Fri, 26 Jun 2020 09:29:56: 25000000 INFO @ Fri, 26 Jun 2020 09:30:00: 30000000 INFO @ Fri, 26 Jun 2020 09:30:03: 26000000 INFO @ Fri, 26 Jun 2020 09:30:07: 31000000 INFO @ Fri, 26 Jun 2020 09:30:09: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:30:14: 32000000 INFO @ Fri, 26 Jun 2020 09:30:16: 28000000 INFO @ Fri, 26 Jun 2020 09:30:20: 33000000 INFO @ Fri, 26 Jun 2020 09:30:22: 29000000 INFO @ Fri, 26 Jun 2020 09:30:27: 34000000 INFO @ Fri, 26 Jun 2020 09:30:29: 30000000 INFO @ Fri, 26 Jun 2020 09:30:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:30:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:30:29: #1 total tags in treatment: 34232175 INFO @ Fri, 26 Jun 2020 09:30:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:30:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:30:29: #1 tags after filtering in treatment: 34232175 INFO @ Fri, 26 Jun 2020 09:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:30:29: #1 finished! INFO @ Fri, 26 Jun 2020 09:30:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:30:32: #2 number of paired peaks: 212 WARNING @ Fri, 26 Jun 2020 09:30:32: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Fri, 26 Jun 2020 09:30:32: start model_add_line... INFO @ Fri, 26 Jun 2020 09:30:32: start X-correlation... INFO @ Fri, 26 Jun 2020 09:30:32: end of X-cor INFO @ Fri, 26 Jun 2020 09:30:32: #2 finished! INFO @ Fri, 26 Jun 2020 09:30:32: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 09:30:32: #2 alternative fragment length(s) may be 1,50,114,127,566 bps INFO @ Fri, 26 Jun 2020 09:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.10_model.r WARNING @ Fri, 26 Jun 2020 09:30:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:30:32: #2 You may need to consider one of the other alternative d(s): 1,50,114,127,566 WARNING @ Fri, 26 Jun 2020 09:30:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:30:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:30:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:30:35: 31000000 INFO @ Fri, 26 Jun 2020 09:30:41: 32000000 INFO @ Fri, 26 Jun 2020 09:30:47: 33000000 INFO @ Fri, 26 Jun 2020 09:30:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:30:53: 34000000 INFO @ Fri, 26 Jun 2020 09:30:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:30:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:30:54: #1 total tags in treatment: 34232175 INFO @ Fri, 26 Jun 2020 09:30:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:30:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:30:55: #1 tags after filtering in treatment: 34232175 INFO @ Fri, 26 Jun 2020 09:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:30:55: #1 finished! INFO @ Fri, 26 Jun 2020 09:30:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:30:57: #2 number of paired peaks: 212 WARNING @ Fri, 26 Jun 2020 09:30:57: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Fri, 26 Jun 2020 09:30:57: start model_add_line... INFO @ Fri, 26 Jun 2020 09:30:57: start X-correlation... INFO @ Fri, 26 Jun 2020 09:30:57: end of X-cor INFO @ Fri, 26 Jun 2020 09:30:57: #2 finished! INFO @ Fri, 26 Jun 2020 09:30:57: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 09:30:57: #2 alternative fragment length(s) may be 1,50,114,127,566 bps INFO @ Fri, 26 Jun 2020 09:30:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.20_model.r WARNING @ Fri, 26 Jun 2020 09:30:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:30:57: #2 You may need to consider one of the other alternative d(s): 1,50,114,127,566 WARNING @ Fri, 26 Jun 2020 09:30:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:30:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.05_summits.bed INFO @ Fri, 26 Jun 2020 09:31:13: 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。 INFO @ Fri, 26 Jun 2020 09:31:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:31:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:31:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:31:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:31:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.10_summits.bed INFO @ Fri, 26 Jun 2020 09:31:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:32:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:32:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:32:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685467/SRX685467.20_summits.bed INFO @ Fri, 26 Jun 2020 09:32:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling