Job ID = 6458873 SRX = SRX5717042 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:45:22 prefetch.2.10.7: 1) Downloading 'SRR8936403'... 2020-06-21T12:45:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:47:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:47:46 prefetch.2.10.7: 1) 'SRR8936403' was downloaded successfully Read 23337741 spots for SRR8936403/SRR8936403.sra Written 23337741 spots for SRR8936403/SRR8936403.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: 00:05:26 23337741 reads; of these: 23337741 (100.00%) were unpaired; of these: 1266712 (5.43%) aligned 0 times 17449238 (74.77%) aligned exactly 1 time 4621791 (19.80%) aligned >1 times 94.57% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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 12 files... [bam_rmdupse_core] 6759778 / 22071029 = 0.3063 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 21:58:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.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 21:58:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:33: 1000000 INFO @ Sun, 21 Jun 2020 21:58:38: 2000000 INFO @ Sun, 21 Jun 2020 21:58:44: 3000000 INFO @ Sun, 21 Jun 2020 21:58:49: 4000000 INFO @ Sun, 21 Jun 2020 21:58:55: 5000000 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 21:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.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 21:58:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:00: 6000000 INFO @ Sun, 21 Jun 2020 21:59:03: 1000000 INFO @ Sun, 21 Jun 2020 21:59:06: 7000000 INFO @ Sun, 21 Jun 2020 21:59:09: 2000000 INFO @ Sun, 21 Jun 2020 21:59:12: 8000000 INFO @ Sun, 21 Jun 2020 21:59:15: 3000000 INFO @ Sun, 21 Jun 2020 21:59:18: 9000000 INFO @ Sun, 21 Jun 2020 21:59:21: 4000000 INFO @ Sun, 21 Jun 2020 21:59:23: 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 @ Sun, 21 Jun 2020 21:59:27: 5000000 INFO @ Sun, 21 Jun 2020 21:59:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.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 21:59:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:29: 11000000 INFO @ Sun, 21 Jun 2020 21:59:33: 6000000 INFO @ Sun, 21 Jun 2020 21:59:33: 1000000 INFO @ Sun, 21 Jun 2020 21:59:35: 12000000 INFO @ Sun, 21 Jun 2020 21:59:39: 7000000 INFO @ Sun, 21 Jun 2020 21:59:39: 2000000 INFO @ Sun, 21 Jun 2020 21:59:41: 13000000 INFO @ Sun, 21 Jun 2020 21:59:45: 8000000 INFO @ Sun, 21 Jun 2020 21:59:45: 3000000 INFO @ Sun, 21 Jun 2020 21:59:46: 14000000 INFO @ Sun, 21 Jun 2020 21:59:50: 9000000 INFO @ Sun, 21 Jun 2020 21:59:51: 4000000 INFO @ Sun, 21 Jun 2020 21:59:52: 15000000 INFO @ Sun, 21 Jun 2020 21:59:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:59:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:59:54: #1 total tags in treatment: 15311251 INFO @ Sun, 21 Jun 2020 21:59:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:54: #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 21:59:54: #1 tags after filtering in treatment: 15311171 INFO @ Sun, 21 Jun 2020 21:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:55: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 21:59:55: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:56: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 21:59:56: #2 alternative fragment length(s) may be 21,56,70,98,120,124,154,197,217,319,426,450,477,497,557,578,598 bps INFO @ Sun, 21 Jun 2020 21:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.05_model.r WARNING @ Sun, 21 Jun 2020 21:59:56: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:56: #2 You may need to consider one of the other alternative d(s): 21,56,70,98,120,124,154,197,217,319,426,450,477,497,557,578,598 WARNING @ Sun, 21 Jun 2020 21:59:56: #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 21:59:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:56: 10000000 INFO @ Sun, 21 Jun 2020 21:59:57: 5000000 INFO @ Sun, 21 Jun 2020 22:00:02: 11000000 INFO @ Sun, 21 Jun 2020 22:00:02: 6000000 INFO @ Sun, 21 Jun 2020 22:00:08: 12000000 INFO @ Sun, 21 Jun 2020 22:00:08: 7000000 INFO @ Sun, 21 Jun 2020 22:00:14: 8000000 INFO @ Sun, 21 Jun 2020 22:00:14: 13000000 INFO @ Sun, 21 Jun 2020 22:00:20: 9000000 INFO @ Sun, 21 Jun 2020 22:00:20: 14000000 INFO @ Sun, 21 Jun 2020 22:00:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:25: 10000000 INFO @ Sun, 21 Jun 2020 22:00:26: 15000000 INFO @ Sun, 21 Jun 2020 22:00:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:00:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:00:28: #1 total tags in treatment: 15311251 INFO @ Sun, 21 Jun 2020 22:00:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:28: #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 22:00:28: #1 tags after filtering in treatment: 15311171 INFO @ Sun, 21 Jun 2020 22:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:29: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 22:00:29: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:29: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:29: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:29: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:29: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:29: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 22:00:29: #2 alternative fragment length(s) may be 21,56,70,98,120,124,154,197,217,319,426,450,477,497,557,578,598 bps INFO @ Sun, 21 Jun 2020 22:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.10_model.r WARNING @ Sun, 21 Jun 2020 22:00:29: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:29: #2 You may need to consider one of the other alternative d(s): 21,56,70,98,120,124,154,197,217,319,426,450,477,497,557,578,598 WARNING @ Sun, 21 Jun 2020 22:00:29: #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 22:00:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:31: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:00:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.05_summits.bed INFO @ Sun, 21 Jun 2020 22:00:36: Done! INFO @ Sun, 21 Jun 2020 22:00:37: 12000000 pass1 - making usageList (295 chroms): 1 millis pass2 - checking and writing primary data (1047 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:43: 13000000 INFO @ Sun, 21 Jun 2020 22:00:48: 14000000 INFO @ Sun, 21 Jun 2020 22:00:54: 15000000 INFO @ Sun, 21 Jun 2020 22:00:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:00:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:00:56: #1 total tags in treatment: 15311251 INFO @ Sun, 21 Jun 2020 22:00:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:56: #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 22:00:56: #1 tags after filtering in treatment: 15311171 INFO @ Sun, 21 Jun 2020 22:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:57: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 22:00:57: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:57: #2 predicted fragment length is 70 bps INFO @ Sun, 21 Jun 2020 22:00:57: #2 alternative fragment length(s) may be 21,56,70,98,120,124,154,197,217,319,426,450,477,497,557,578,598 bps INFO @ Sun, 21 Jun 2020 22:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.20_model.r WARNING @ Sun, 21 Jun 2020 22:00:57: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:57: #2 You may need to consider one of the other alternative d(s): 21,56,70,98,120,124,154,197,217,319,426,450,477,497,557,578,598 WARNING @ Sun, 21 Jun 2020 22:00:57: #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 22:00:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:01:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.10_summits.bed INFO @ Sun, 21 Jun 2020 22:01:11: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:01:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717042/SRX5717042.20_summits.bed INFO @ Sun, 21 Jun 2020 22:01:43: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 3 millis CompletedMACS2peakCalling