Job ID = 14170378 SRX = SRX8689002 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20445519 spots for SRR12174233/SRR12174233.sra Written 20445519 spots for SRR12174233/SRR12174233.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170779 ("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: 00:07:20 20445519 reads; of these: 20445519 (100.00%) were unpaired; of these: 645930 (3.16%) aligned 0 times 13543051 (66.24%) aligned exactly 1 time 6256538 (30.60%) aligned >1 times 96.84% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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] 1789456 / 19799589 = 0.0904 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 06:40:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.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 06:40:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:37: 1000000 INFO @ Sat, 11 Dec 2021 06:40:42: 2000000 INFO @ Sat, 11 Dec 2021 06:40:47: 3000000 INFO @ Sat, 11 Dec 2021 06:40:52: 4000000 INFO @ Sat, 11 Dec 2021 06:40:57: 5000000 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 06:41:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.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 06:41:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:41:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:41:03: 6000000 INFO @ Sat, 11 Dec 2021 06:41:08: 7000000 INFO @ Sat, 11 Dec 2021 06:41:08: 1000000 INFO @ Sat, 11 Dec 2021 06:41:14: 8000000 INFO @ Sat, 11 Dec 2021 06:41:14: 2000000 INFO @ Sat, 11 Dec 2021 06:41:19: 9000000 INFO @ Sat, 11 Dec 2021 06:41:21: 3000000 INFO @ Sat, 11 Dec 2021 06:41:25: 10000000 INFO @ Sat, 11 Dec 2021 06:41:27: 4000000 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 06:41:30: 11000000 INFO @ Sat, 11 Dec 2021 06:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.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 06:41:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:41:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:41:33: 5000000 INFO @ Sat, 11 Dec 2021 06:41:36: 12000000 INFO @ Sat, 11 Dec 2021 06:41:38: 1000000 INFO @ Sat, 11 Dec 2021 06:41:39: 6000000 INFO @ Sat, 11 Dec 2021 06:41:41: 13000000 INFO @ Sat, 11 Dec 2021 06:41:43: 2000000 INFO @ Sat, 11 Dec 2021 06:41:46: 7000000 INFO @ Sat, 11 Dec 2021 06:41:47: 14000000 INFO @ Sat, 11 Dec 2021 06:41:49: 3000000 INFO @ Sat, 11 Dec 2021 06:41:52: 8000000 INFO @ Sat, 11 Dec 2021 06:41:52: 15000000 INFO @ Sat, 11 Dec 2021 06:41:55: 4000000 INFO @ Sat, 11 Dec 2021 06:41:58: 16000000 INFO @ Sat, 11 Dec 2021 06:41:58: 9000000 INFO @ Sat, 11 Dec 2021 06:42:00: 5000000 INFO @ Sat, 11 Dec 2021 06:42:03: 17000000 INFO @ Sat, 11 Dec 2021 06:42:04: 10000000 INFO @ Sat, 11 Dec 2021 06:42:06: 6000000 INFO @ Sat, 11 Dec 2021 06:42:09: 18000000 INFO @ Sat, 11 Dec 2021 06:42:09: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:09: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:09: #1 total tags in treatment: 18010133 INFO @ Sat, 11 Dec 2021 06:42:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:09: #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 06:42:09: #1 tags after filtering in treatment: 18010133 INFO @ Sat, 11 Dec 2021 06:42:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:09: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:11: #2 number of paired peaks: 101 WARNING @ Sat, 11 Dec 2021 06:42:11: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:11: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:11: 11000000 INFO @ Sat, 11 Dec 2021 06:42:11: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:11: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:11: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:11: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 06:42:11: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 11 Dec 2021 06:42:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.05_model.r WARNING @ Sat, 11 Dec 2021 06:42:11: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:42:11: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 11 Dec 2021 06:42:11: #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 06:42:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:12: 7000000 INFO @ Sat, 11 Dec 2021 06:42:17: 12000000 INFO @ Sat, 11 Dec 2021 06:42:17: 8000000 INFO @ Sat, 11 Dec 2021 06:42:23: 9000000 INFO @ Sat, 11 Dec 2021 06:42:23: 13000000 INFO @ Sat, 11 Dec 2021 06:42:29: 10000000 INFO @ Sat, 11 Dec 2021 06:42:29: 14000000 INFO @ Sat, 11 Dec 2021 06:42:34: 11000000 INFO @ Sat, 11 Dec 2021 06:42:35: 15000000 INFO @ Sat, 11 Dec 2021 06:42:40: 12000000 INFO @ Sat, 11 Dec 2021 06:42:42: 16000000 INFO @ Sat, 11 Dec 2021 06:42:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:42:45: 13000000 INFO @ Sat, 11 Dec 2021 06:42:48: 17000000 INFO @ Sat, 11 Dec 2021 06:42:51: 14000000 INFO @ Sat, 11 Dec 2021 06:42:54: 18000000 INFO @ Sat, 11 Dec 2021 06:42:54: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:54: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:54: #1 total tags in treatment: 18010133 INFO @ Sat, 11 Dec 2021 06:42:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:54: #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 06:42:55: #1 tags after filtering in treatment: 18010133 INFO @ Sat, 11 Dec 2021 06:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:55: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:55: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:42:56: #2 number of paired peaks: 101 WARNING @ Sat, 11 Dec 2021 06:42:56: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:56: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:56: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:56: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:56: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:56: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 06:42:56: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 11 Dec 2021 06:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.10_model.r WARNING @ Sat, 11 Dec 2021 06:42:56: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:42:56: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 11 Dec 2021 06:42:56: #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 06:42:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:57: 15000000 INFO @ Sat, 11 Dec 2021 06:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.05_summits.bed INFO @ Sat, 11 Dec 2021 06:43:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1981 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:43:02: 16000000 INFO @ Sat, 11 Dec 2021 06:43:07: 17000000 INFO @ Sat, 11 Dec 2021 06:43:13: 18000000 INFO @ Sat, 11 Dec 2021 06:43:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:43:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:43:13: #1 total tags in treatment: 18010133 INFO @ Sat, 11 Dec 2021 06:43:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:43:13: #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 06:43:13: #1 tags after filtering in treatment: 18010133 INFO @ Sat, 11 Dec 2021 06:43:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:43:13: #1 finished! INFO @ Sat, 11 Dec 2021 06:43:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:43:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:43:14: #2 number of paired peaks: 101 WARNING @ Sat, 11 Dec 2021 06:43:14: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 11 Dec 2021 06:43:14: start model_add_line... INFO @ Sat, 11 Dec 2021 06:43:14: start X-correlation... INFO @ Sat, 11 Dec 2021 06:43:14: end of X-cor INFO @ Sat, 11 Dec 2021 06:43:14: #2 finished! INFO @ Sat, 11 Dec 2021 06:43:14: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 06:43:14: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 11 Dec 2021 06:43:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.20_model.r WARNING @ Sat, 11 Dec 2021 06:43:14: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:43:14: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 11 Dec 2021 06:43:14: #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 06:43:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:43:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:43:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.10_summits.bed INFO @ Sat, 11 Dec 2021 06:43:46: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1444 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:43:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:44:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:44:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:44:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689002/SRX8689002.20_summits.bed INFO @ Sat, 11 Dec 2021 06:44:05: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (991 records, 4 fields): 3 millis CompletedMACS2peakCalling