Job ID = 6529329 SRX = SRX1837299 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:20 34731005 reads; of these: 34731005 (100.00%) were unpaired; of these: 1239647 (3.57%) aligned 0 times 17927917 (51.62%) aligned exactly 1 time 15563441 (44.81%) aligned >1 times 96.43% overall alignment rate Time searching: 00:13:21 Overall time: 00:13:21 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] 14216165 / 33491358 = 0.4245 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 @ Tue, 30 Jun 2020 02:03:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.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 @ Tue, 30 Jun 2020 02:03:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:03:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:02: 1000000 INFO @ Tue, 30 Jun 2020 02:04:08: 2000000 INFO @ Tue, 30 Jun 2020 02:04:14: 3000000 INFO @ Tue, 30 Jun 2020 02:04:19: 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 @ Tue, 30 Jun 2020 02:04:25: 5000000 INFO @ Tue, 30 Jun 2020 02:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.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 @ Tue, 30 Jun 2020 02:04:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:31: 6000000 INFO @ Tue, 30 Jun 2020 02:04:32: 1000000 INFO @ Tue, 30 Jun 2020 02:04:36: 7000000 INFO @ Tue, 30 Jun 2020 02:04:38: 2000000 INFO @ Tue, 30 Jun 2020 02:04:42: 8000000 INFO @ Tue, 30 Jun 2020 02:04:44: 3000000 INFO @ Tue, 30 Jun 2020 02:04:47: 9000000 INFO @ Tue, 30 Jun 2020 02:04:50: 4000000 INFO @ Tue, 30 Jun 2020 02:04:54: 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 @ Tue, 30 Jun 2020 02:04:56: 5000000 INFO @ Tue, 30 Jun 2020 02:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.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 @ Tue, 30 Jun 2020 02:04:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:00: 11000000 INFO @ Tue, 30 Jun 2020 02:05:02: 6000000 INFO @ Tue, 30 Jun 2020 02:05:03: 1000000 INFO @ Tue, 30 Jun 2020 02:05:06: 12000000 INFO @ Tue, 30 Jun 2020 02:05:08: 7000000 INFO @ Tue, 30 Jun 2020 02:05:09: 2000000 INFO @ Tue, 30 Jun 2020 02:05:12: 13000000 INFO @ Tue, 30 Jun 2020 02:05:14: 8000000 INFO @ Tue, 30 Jun 2020 02:05:15: 3000000 INFO @ Tue, 30 Jun 2020 02:05:17: 14000000 INFO @ Tue, 30 Jun 2020 02:05:20: 9000000 INFO @ Tue, 30 Jun 2020 02:05:21: 4000000 INFO @ Tue, 30 Jun 2020 02:05:24: 15000000 INFO @ Tue, 30 Jun 2020 02:05:26: 10000000 INFO @ Tue, 30 Jun 2020 02:05:28: 5000000 INFO @ Tue, 30 Jun 2020 02:05:30: 16000000 INFO @ Tue, 30 Jun 2020 02:05:32: 11000000 INFO @ Tue, 30 Jun 2020 02:05:34: 6000000 INFO @ Tue, 30 Jun 2020 02:05:36: 17000000 INFO @ Tue, 30 Jun 2020 02:05:39: 12000000 INFO @ Tue, 30 Jun 2020 02:05:40: 7000000 INFO @ Tue, 30 Jun 2020 02:05:42: 18000000 INFO @ Tue, 30 Jun 2020 02:05:45: 13000000 INFO @ Tue, 30 Jun 2020 02:05:46: 8000000 INFO @ Tue, 30 Jun 2020 02:05:48: 19000000 INFO @ Tue, 30 Jun 2020 02:05:50: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:05:50: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:05:50: #1 total tags in treatment: 19275193 INFO @ Tue, 30 Jun 2020 02:05:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:05:51: 14000000 INFO @ Tue, 30 Jun 2020 02:05:51: #1 tags after filtering in treatment: 19275140 INFO @ Tue, 30 Jun 2020 02:05:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:51: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:52: 9000000 INFO @ Tue, 30 Jun 2020 02:05:53: #2 number of paired peaks: 1815 INFO @ Tue, 30 Jun 2020 02:05:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:53: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:05:53: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 30 Jun 2020 02:05:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.05_model.r WARNING @ Tue, 30 Jun 2020 02:05:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:05:53: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 30 Jun 2020 02:05:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:05:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:58: 15000000 INFO @ Tue, 30 Jun 2020 02:05:59: 10000000 INFO @ Tue, 30 Jun 2020 02:06:04: 16000000 INFO @ Tue, 30 Jun 2020 02:06:05: 11000000 INFO @ Tue, 30 Jun 2020 02:06:10: 17000000 INFO @ Tue, 30 Jun 2020 02:06:11: 12000000 INFO @ Tue, 30 Jun 2020 02:06:16: 18000000 INFO @ Tue, 30 Jun 2020 02:06:17: 13000000 INFO @ Tue, 30 Jun 2020 02:06:22: 19000000 INFO @ Tue, 30 Jun 2020 02:06:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:23: 14000000 INFO @ Tue, 30 Jun 2020 02:06:24: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:06:24: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:06:24: #1 total tags in treatment: 19275193 INFO @ Tue, 30 Jun 2020 02:06:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:06:25: #1 tags after filtering in treatment: 19275140 INFO @ Tue, 30 Jun 2020 02:06:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:26: #2 number of paired peaks: 1815 INFO @ Tue, 30 Jun 2020 02:06:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:26: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:06:26: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 30 Jun 2020 02:06:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.10_model.r WARNING @ Tue, 30 Jun 2020 02:06:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:26: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 30 Jun 2020 02:06:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:06:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:29: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:06:35: 16000000 INFO @ Tue, 30 Jun 2020 02:06:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.05_summits.bed INFO @ Tue, 30 Jun 2020 02:06:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:06:40: 17000000 INFO @ Tue, 30 Jun 2020 02:06:46: 18000000 INFO @ Tue, 30 Jun 2020 02:06:52: 19000000 INFO @ Tue, 30 Jun 2020 02:06:54: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:06:54: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:06:54: #1 total tags in treatment: 19275193 INFO @ Tue, 30 Jun 2020 02:06:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:06:55: #1 tags after filtering in treatment: 19275140 INFO @ Tue, 30 Jun 2020 02:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:55: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:56: #2 number of paired peaks: 1815 INFO @ Tue, 30 Jun 2020 02:06:56: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:56: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:56: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:56: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:56: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:06:56: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 30 Jun 2020 02:06:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.20_model.r WARNING @ Tue, 30 Jun 2020 02:06:56: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:56: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 30 Jun 2020 02:06:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:06:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.10_summits.bed INFO @ Tue, 30 Jun 2020 02:07:11: 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 @ Tue, 30 Jun 2020 02:07:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837299/SRX1837299.20_summits.bed INFO @ Tue, 30 Jun 2020 02:07:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling