Job ID = 16437941 SRX = SRX14148452 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17047876 spots for SRR17992818/SRR17992818.sra Written 17047876 spots for SRR17992818/SRR17992818.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438077 ("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: 00:10:58 17047876 reads; of these: 17047876 (100.00%) were unpaired; of these: 821818 (4.82%) aligned 0 times 11369052 (66.69%) aligned exactly 1 time 4857006 (28.49%) aligned >1 times 95.18% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 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] 1771553 / 16226058 = 0.1092 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.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, 02 Aug 2022 13:32:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:32:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:33:04: 1000000 INFO @ Tue, 02 Aug 2022 13:33:11: 2000000 INFO @ Tue, 02 Aug 2022 13:33:19: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:33:27: 4000000 INFO @ Tue, 02 Aug 2022 13:33:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.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, 02 Aug 2022 13:33:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:33:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:33:36: 1000000 INFO @ Tue, 02 Aug 2022 13:33:36: 5000000 INFO @ Tue, 02 Aug 2022 13:33:45: 2000000 INFO @ Tue, 02 Aug 2022 13:33:45: 6000000 INFO @ Tue, 02 Aug 2022 13:33:54: 7000000 INFO @ Tue, 02 Aug 2022 13:33:55: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.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, 02 Aug 2022 13:33:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:33:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:34:03: 8000000 INFO @ Tue, 02 Aug 2022 13:34:05: 4000000 INFO @ Tue, 02 Aug 2022 13:34:07: 1000000 INFO @ Tue, 02 Aug 2022 13:34:13: 9000000 INFO @ Tue, 02 Aug 2022 13:34:15: 5000000 INFO @ Tue, 02 Aug 2022 13:34:18: 2000000 INFO @ Tue, 02 Aug 2022 13:34:23: 10000000 INFO @ Tue, 02 Aug 2022 13:34:25: 6000000 INFO @ Tue, 02 Aug 2022 13:34:28: 3000000 INFO @ Tue, 02 Aug 2022 13:34:32: 11000000 INFO @ Tue, 02 Aug 2022 13:34:36: 7000000 INFO @ Tue, 02 Aug 2022 13:34:38: 4000000 INFO @ Tue, 02 Aug 2022 13:34:40: 12000000 INFO @ Tue, 02 Aug 2022 13:34:46: 8000000 INFO @ Tue, 02 Aug 2022 13:34:48: 5000000 INFO @ Tue, 02 Aug 2022 13:34:48: 13000000 INFO @ Tue, 02 Aug 2022 13:34:56: 9000000 INFO @ Tue, 02 Aug 2022 13:34:58: 14000000 INFO @ Tue, 02 Aug 2022 13:34:58: 6000000 INFO @ Tue, 02 Aug 2022 13:35:02: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:35:02: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:35:02: #1 total tags in treatment: 14454505 INFO @ Tue, 02 Aug 2022 13:35:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:35:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:35:02: #1 tags after filtering in treatment: 14454505 INFO @ Tue, 02 Aug 2022 13:35:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:35:02: #1 finished! INFO @ Tue, 02 Aug 2022 13:35:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:35:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:35:03: #2 number of paired peaks: 629 WARNING @ Tue, 02 Aug 2022 13:35:03: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Tue, 02 Aug 2022 13:35:03: start model_add_line... INFO @ Tue, 02 Aug 2022 13:35:04: start X-correlation... INFO @ Tue, 02 Aug 2022 13:35:04: end of X-cor INFO @ Tue, 02 Aug 2022 13:35:04: #2 finished! INFO @ Tue, 02 Aug 2022 13:35:04: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:35:04: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 13:35:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.05_model.r WARNING @ Tue, 02 Aug 2022 13:35:04: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:35:04: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 13:35:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:35:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:35:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:35:05: 10000000 INFO @ Tue, 02 Aug 2022 13:35:07: 7000000 INFO @ Tue, 02 Aug 2022 13:35:15: 11000000 INFO @ Tue, 02 Aug 2022 13:35:17: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:35:24: 12000000 INFO @ Tue, 02 Aug 2022 13:35:26: 9000000 INFO @ Tue, 02 Aug 2022 13:35:33: 13000000 INFO @ Tue, 02 Aug 2022 13:35:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:35:35: 10000000 INFO @ Tue, 02 Aug 2022 13:35:45: 14000000 INFO @ Tue, 02 Aug 2022 13:35:46: 11000000 INFO @ Tue, 02 Aug 2022 13:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:35:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.05_summits.bed INFO @ Tue, 02 Aug 2022 13:35:49: Done! pass1 - making usageList (15 chroms): 34 millis pass2 - checking and writing primary data (2663 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:35:51: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:35:51: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:35:51: #1 total tags in treatment: 14454505 INFO @ Tue, 02 Aug 2022 13:35:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:35:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:35:52: #1 tags after filtering in treatment: 14454505 INFO @ Tue, 02 Aug 2022 13:35:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:35:52: #1 finished! INFO @ Tue, 02 Aug 2022 13:35:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:35:53: #2 number of paired peaks: 629 WARNING @ Tue, 02 Aug 2022 13:35:53: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Tue, 02 Aug 2022 13:35:53: start model_add_line... INFO @ Tue, 02 Aug 2022 13:35:53: start X-correlation... INFO @ Tue, 02 Aug 2022 13:35:53: end of X-cor INFO @ Tue, 02 Aug 2022 13:35:53: #2 finished! INFO @ Tue, 02 Aug 2022 13:35:53: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:35:53: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 13:35:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.10_model.r WARNING @ Tue, 02 Aug 2022 13:35:53: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:35:53: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 13:35:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:35:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:35:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:35:55: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:36:04: 13000000 INFO @ Tue, 02 Aug 2022 13:36:12: 14000000 INFO @ Tue, 02 Aug 2022 13:36:16: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:36:16: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:36:16: #1 total tags in treatment: 14454505 INFO @ Tue, 02 Aug 2022 13:36:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:36:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:36:16: #1 tags after filtering in treatment: 14454505 INFO @ Tue, 02 Aug 2022 13:36:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:36:16: #1 finished! INFO @ Tue, 02 Aug 2022 13:36:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:36:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:36:17: #2 number of paired peaks: 629 WARNING @ Tue, 02 Aug 2022 13:36:17: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Tue, 02 Aug 2022 13:36:17: start model_add_line... INFO @ Tue, 02 Aug 2022 13:36:17: start X-correlation... INFO @ Tue, 02 Aug 2022 13:36:17: end of X-cor INFO @ Tue, 02 Aug 2022 13:36:17: #2 finished! INFO @ Tue, 02 Aug 2022 13:36:17: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:36:17: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 13:36:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.20_model.r WARNING @ Tue, 02 Aug 2022 13:36:18: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:36:18: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 13:36:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:36:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:36:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.10_summits.bed INFO @ Tue, 02 Aug 2022 13:36:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1692 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:36:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148452/SRX14148452.20_summits.bed INFO @ Tue, 02 Aug 2022 13:37:03: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (865 records, 4 fields): 34 millis CompletedMACS2peakCalling