Job ID = 14170365 SRX = SRX9720900 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27242850 spots for SRR13291890/SRR13291890.sra Written 27242850 spots for SRR13291890/SRR13291890.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170767 ("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: 00:10:24 27242850 reads; of these: 27242850 (100.00%) were unpaired; of these: 851723 (3.13%) aligned 0 times 18389479 (67.50%) aligned exactly 1 time 8001648 (29.37%) aligned >1 times 96.87% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 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 12 files... [bam_rmdupse_core] 5690348 / 26391127 = 0.2156 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 06:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.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 06:39:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:39: 1000000 INFO @ Sat, 11 Dec 2021 06:39:47: 2000000 INFO @ Sat, 11 Dec 2021 06:39:57: 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 06:40:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.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 06:40:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:06: 4000000 INFO @ Sat, 11 Dec 2021 06:40:09: 1000000 INFO @ Sat, 11 Dec 2021 06:40:15: 5000000 INFO @ Sat, 11 Dec 2021 06:40:19: 2000000 INFO @ Sat, 11 Dec 2021 06:40:24: 6000000 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 06:40:28: 3000000 INFO @ Sat, 11 Dec 2021 06:40:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.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 06:40:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:33: 7000000 INFO @ Sat, 11 Dec 2021 06:40:38: 4000000 INFO @ Sat, 11 Dec 2021 06:40:39: 1000000 INFO @ Sat, 11 Dec 2021 06:40:43: 8000000 INFO @ Sat, 11 Dec 2021 06:40:47: 5000000 INFO @ Sat, 11 Dec 2021 06:40:47: 2000000 INFO @ Sat, 11 Dec 2021 06:40:52: 9000000 INFO @ Sat, 11 Dec 2021 06:40:56: 3000000 INFO @ Sat, 11 Dec 2021 06:40:56: 6000000 INFO @ Sat, 11 Dec 2021 06:41:01: 10000000 INFO @ Sat, 11 Dec 2021 06:41:05: 4000000 INFO @ Sat, 11 Dec 2021 06:41:06: 7000000 INFO @ Sat, 11 Dec 2021 06:41:10: 11000000 INFO @ Sat, 11 Dec 2021 06:41:13: 5000000 INFO @ Sat, 11 Dec 2021 06:41:15: 8000000 INFO @ Sat, 11 Dec 2021 06:41:19: 12000000 INFO @ Sat, 11 Dec 2021 06:41:22: 6000000 INFO @ Sat, 11 Dec 2021 06:41:24: 9000000 INFO @ Sat, 11 Dec 2021 06:41:28: 13000000 INFO @ Sat, 11 Dec 2021 06:41:30: 7000000 INFO @ Sat, 11 Dec 2021 06:41:34: 10000000 INFO @ Sat, 11 Dec 2021 06:41:37: 14000000 INFO @ Sat, 11 Dec 2021 06:41:39: 8000000 INFO @ Sat, 11 Dec 2021 06:41:43: 11000000 INFO @ Sat, 11 Dec 2021 06:41:46: 15000000 INFO @ Sat, 11 Dec 2021 06:41:47: 9000000 INFO @ Sat, 11 Dec 2021 06:41:52: 12000000 INFO @ Sat, 11 Dec 2021 06:41:55: 16000000 INFO @ Sat, 11 Dec 2021 06:41:56: 10000000 INFO @ Sat, 11 Dec 2021 06:42:01: 13000000 INFO @ Sat, 11 Dec 2021 06:42:04: 11000000 INFO @ Sat, 11 Dec 2021 06:42:05: 17000000 INFO @ Sat, 11 Dec 2021 06:42:10: 14000000 INFO @ Sat, 11 Dec 2021 06:42:13: 12000000 INFO @ Sat, 11 Dec 2021 06:42:14: 18000000 INFO @ Sat, 11 Dec 2021 06:42:19: 15000000 INFO @ Sat, 11 Dec 2021 06:42:21: 13000000 INFO @ Sat, 11 Dec 2021 06:42:24: 19000000 INFO @ Sat, 11 Dec 2021 06:42:29: 16000000 INFO @ Sat, 11 Dec 2021 06:42:29: 14000000 BedGraph に変換しました。 INFO @ Sat, 11 Dec 2021 06:42:33: 20000000 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:42:38: 15000000 INFO @ Sat, 11 Dec 2021 06:42:39: 17000000 INFO @ Sat, 11 Dec 2021 06:42:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:39: #1 total tags in treatment: 20700779 INFO @ Sat, 11 Dec 2021 06:42:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:39: #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 06:42:40: #1 tags after filtering in treatment: 20700779 INFO @ Sat, 11 Dec 2021 06:42:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:40: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:41: #2 number of paired peaks: 410 WARNING @ Sat, 11 Dec 2021 06:42:41: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:41: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:41: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:41: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:41: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:41: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Dec 2021 06:42:41: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sat, 11 Dec 2021 06:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.05_model.r WARNING @ Sat, 11 Dec 2021 06:42:41: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:42:41: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sat, 11 Dec 2021 06:42:41: #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 06:42:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:46: 16000000 INFO @ Sat, 11 Dec 2021 06:42:47: 18000000 INFO @ Sat, 11 Dec 2021 06:42:55: 17000000 INFO @ Sat, 11 Dec 2021 06:42:56: 19000000 INFO @ Sat, 11 Dec 2021 06:43:03: 18000000 INFO @ Sat, 11 Dec 2021 06:43:05: 20000000 INFO @ Sat, 11 Dec 2021 06:43:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:43:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:43:11: #1 total tags in treatment: 20700779 INFO @ Sat, 11 Dec 2021 06:43:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:43:11: #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 06:43:11: #1 tags after filtering in treatment: 20700779 INFO @ Sat, 11 Dec 2021 06:43:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:43:11: #1 finished! INFO @ Sat, 11 Dec 2021 06:43:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:43:11: 19000000 INFO @ Sat, 11 Dec 2021 06:43:13: #2 number of paired peaks: 410 WARNING @ Sat, 11 Dec 2021 06:43:13: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Sat, 11 Dec 2021 06:43:13: start model_add_line... INFO @ Sat, 11 Dec 2021 06:43:13: start X-correlation... INFO @ Sat, 11 Dec 2021 06:43:13: end of X-cor INFO @ Sat, 11 Dec 2021 06:43:13: #2 finished! INFO @ Sat, 11 Dec 2021 06:43:13: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Dec 2021 06:43:13: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sat, 11 Dec 2021 06:43:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.10_model.r WARNING @ Sat, 11 Dec 2021 06:43:13: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:43:13: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sat, 11 Dec 2021 06:43:13: #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 06:43:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:43:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:43:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:43:20: 20000000 INFO @ Sat, 11 Dec 2021 06:43:25: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:43:25: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:43:25: #1 total tags in treatment: 20700779 INFO @ Sat, 11 Dec 2021 06:43:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:43:25: #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 06:43:26: #1 tags after filtering in treatment: 20700779 INFO @ Sat, 11 Dec 2021 06:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:43:26: #1 finished! INFO @ Sat, 11 Dec 2021 06:43:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:43:27: #2 number of paired peaks: 410 WARNING @ Sat, 11 Dec 2021 06:43:27: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Sat, 11 Dec 2021 06:43:27: start model_add_line... INFO @ Sat, 11 Dec 2021 06:43:27: start X-correlation... INFO @ Sat, 11 Dec 2021 06:43:28: end of X-cor INFO @ Sat, 11 Dec 2021 06:43:28: #2 finished! INFO @ Sat, 11 Dec 2021 06:43:28: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Dec 2021 06:43:28: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sat, 11 Dec 2021 06:43:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.20_model.r WARNING @ Sat, 11 Dec 2021 06:43:28: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:43:28: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sat, 11 Dec 2021 06:43:28: #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 06:43:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:43:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:43:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.05_summits.bed INFO @ Sat, 11 Dec 2021 06:43:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3451 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:43:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:44:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:44:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:44:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:44:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.10_summits.bed INFO @ Sat, 11 Dec 2021 06:44:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2353 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720900/SRX9720900.20_summits.bed INFO @ Sat, 11 Dec 2021 06:44:23: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1179 records, 4 fields): 4 millis CompletedMACS2peakCalling