Job ID = 14170369 SRX = SRX9720904 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19657290 spots for SRR13291894/SRR13291894.sra Written 19657290 spots for SRR13291894/SRR13291894.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170769 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:53 19657290 reads; of these: 19657290 (100.00%) were unpaired; of these: 801968 (4.08%) aligned 0 times 12883233 (65.54%) aligned exactly 1 time 5972089 (30.38%) aligned >1 times 95.92% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 3352421 / 18855322 = 0.1778 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:38:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.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 @ Sat, 11 Dec 2021 06:38:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:38:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:38:47: 1000000 INFO @ Sat, 11 Dec 2021 06:38:55: 2000000 INFO @ Sat, 11 Dec 2021 06:39:02: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:39:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.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 @ Sat, 11 Dec 2021 06:39:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:11: 4000000 INFO @ Sat, 11 Dec 2021 06:39:17: 1000000 INFO @ Sat, 11 Dec 2021 06:39:19: 5000000 INFO @ Sat, 11 Dec 2021 06:39:25: 2000000 INFO @ Sat, 11 Dec 2021 06:39:27: 6000000 INFO @ Sat, 11 Dec 2021 06:39:34: 3000000 INFO @ Sat, 11 Dec 2021 06:39:35: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.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 @ Sat, 11 Dec 2021 06:39:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:42: 4000000 INFO @ Sat, 11 Dec 2021 06:39:43: 8000000 INFO @ Sat, 11 Dec 2021 06:39:46: 1000000 INFO @ Sat, 11 Dec 2021 06:39:51: 5000000 INFO @ Sat, 11 Dec 2021 06:39:51: 9000000 INFO @ Sat, 11 Dec 2021 06:39:54: 2000000 INFO @ Sat, 11 Dec 2021 06:39:59: 6000000 INFO @ Sat, 11 Dec 2021 06:39:59: 10000000 INFO @ Sat, 11 Dec 2021 06:40:01: 3000000 INFO @ Sat, 11 Dec 2021 06:40:07: 7000000 INFO @ Sat, 11 Dec 2021 06:40:07: 11000000 INFO @ Sat, 11 Dec 2021 06:40:08: 4000000 INFO @ Sat, 11 Dec 2021 06:40:15: 12000000 INFO @ Sat, 11 Dec 2021 06:40:15: 8000000 INFO @ Sat, 11 Dec 2021 06:40:16: 5000000 INFO @ Sat, 11 Dec 2021 06:40:23: 6000000 INFO @ Sat, 11 Dec 2021 06:40:23: 13000000 INFO @ Sat, 11 Dec 2021 06:40:23: 9000000 INFO @ Sat, 11 Dec 2021 06:40:30: 7000000 INFO @ Sat, 11 Dec 2021 06:40:31: 14000000 INFO @ Sat, 11 Dec 2021 06:40:32: 10000000 INFO @ Sat, 11 Dec 2021 06:40:38: 8000000 INFO @ Sat, 11 Dec 2021 06:40:40: 15000000 INFO @ Sat, 11 Dec 2021 06:40:40: 11000000 INFO @ Sat, 11 Dec 2021 06:40:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:40:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:40:44: #1 total tags in treatment: 15502901 INFO @ Sat, 11 Dec 2021 06:40:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:40:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:40:44: #1 tags after filtering in treatment: 15502901 INFO @ Sat, 11 Dec 2021 06:40:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:40:44: #1 finished! INFO @ Sat, 11 Dec 2021 06:40:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:40:45: 9000000 INFO @ Sat, 11 Dec 2021 06:40:46: #2 number of paired peaks: 644 WARNING @ Sat, 11 Dec 2021 06:40:46: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Sat, 11 Dec 2021 06:40:46: start model_add_line... INFO @ Sat, 11 Dec 2021 06:40:46: start X-correlation... INFO @ Sat, 11 Dec 2021 06:40:46: end of X-cor INFO @ Sat, 11 Dec 2021 06:40:46: #2 finished! INFO @ Sat, 11 Dec 2021 06:40:46: #2 predicted fragment length is 92 bps INFO @ Sat, 11 Dec 2021 06:40:46: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 11 Dec 2021 06:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.05_model.r WARNING @ Sat, 11 Dec 2021 06:40:46: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:40:46: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 11 Dec 2021 06:40:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:40:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:40:49: 12000000 INFO @ Sat, 11 Dec 2021 06:40:52: 10000000 INFO @ Sat, 11 Dec 2021 06:40:57: 13000000 INFO @ Sat, 11 Dec 2021 06:41:00: 11000000 INFO @ Sat, 11 Dec 2021 06:41:05: 14000000 INFO @ Sat, 11 Dec 2021 06:41:07: 12000000 INFO @ Sat, 11 Dec 2021 06:41:14: 15000000 INFO @ Sat, 11 Dec 2021 06:41:14: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:41:18: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:41:18: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:41:18: #1 total tags in treatment: 15502901 INFO @ Sat, 11 Dec 2021 06:41:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:41:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:41:19: #1 tags after filtering in treatment: 15502901 INFO @ Sat, 11 Dec 2021 06:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:41:19: #1 finished! INFO @ Sat, 11 Dec 2021 06:41:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:41:20: #2 number of paired peaks: 644 WARNING @ Sat, 11 Dec 2021 06:41:20: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Sat, 11 Dec 2021 06:41:20: start model_add_line... INFO @ Sat, 11 Dec 2021 06:41:20: start X-correlation... INFO @ Sat, 11 Dec 2021 06:41:20: end of X-cor INFO @ Sat, 11 Dec 2021 06:41:20: #2 finished! INFO @ Sat, 11 Dec 2021 06:41:20: #2 predicted fragment length is 92 bps INFO @ Sat, 11 Dec 2021 06:41:20: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 11 Dec 2021 06:41:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.10_model.r WARNING @ Sat, 11 Dec 2021 06:41:20: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:41:20: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 11 Dec 2021 06:41:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:41:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:41:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:41:22: 14000000 INFO @ Sat, 11 Dec 2021 06:41:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:41:29: 15000000 INFO @ Sat, 11 Dec 2021 06:41:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:41:33: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:41:33: #1 total tags in treatment: 15502901 INFO @ Sat, 11 Dec 2021 06:41:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:41:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:41:33: #1 tags after filtering in treatment: 15502901 INFO @ Sat, 11 Dec 2021 06:41:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:41:33: #1 finished! INFO @ Sat, 11 Dec 2021 06:41:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:41:35: #2 number of paired peaks: 644 WARNING @ Sat, 11 Dec 2021 06:41:35: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Sat, 11 Dec 2021 06:41:35: start model_add_line... INFO @ Sat, 11 Dec 2021 06:41:35: start X-correlation... INFO @ Sat, 11 Dec 2021 06:41:35: end of X-cor INFO @ Sat, 11 Dec 2021 06:41:35: #2 finished! INFO @ Sat, 11 Dec 2021 06:41:35: #2 predicted fragment length is 92 bps INFO @ Sat, 11 Dec 2021 06:41:35: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 11 Dec 2021 06:41:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.20_model.r WARNING @ Sat, 11 Dec 2021 06:41:35: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:41:35: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 11 Dec 2021 06:41:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:41:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:41:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:41:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:41:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.05_summits.bed INFO @ Sat, 11 Dec 2021 06:41:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4620 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:42:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:42:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.10_summits.bed INFO @ Sat, 11 Dec 2021 06:42:23: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3167 records, 4 fields): 79 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:42:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720904/SRX9720904.20_summits.bed INFO @ Sat, 11 Dec 2021 06:42:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1875 records, 4 fields): 30 millis CompletedMACS2peakCalling