Job ID = 16438119 SRX = SRX14148468 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17448532 spots for SRR17992802/SRR17992802.sra Written 17448532 spots for SRR17992802/SRR17992802.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438511 ("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: 00:09:03 17448532 reads; of these: 17448532 (100.00%) were unpaired; of these: 1014207 (5.81%) aligned 0 times 11883012 (68.10%) aligned exactly 1 time 4551313 (26.08%) aligned >1 times 94.19% overall alignment rate Time searching: 00:09:03 Overall time: 00:09:03 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] 1446928 / 16434325 = 0.0880 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 13:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.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 13:57:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:57:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:57:59: 1000000 INFO @ Tue, 02 Aug 2022 13:58:08: 2000000 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 13:58:16: 3000000 INFO @ Tue, 02 Aug 2022 13:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.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 13:58:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:58:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:58:25: 4000000 INFO @ Tue, 02 Aug 2022 13:58:28: 1000000 INFO @ Tue, 02 Aug 2022 13:58:35: 5000000 INFO @ Tue, 02 Aug 2022 13:58:38: 2000000 INFO @ Tue, 02 Aug 2022 13:58:44: 6000000 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 13:58:47: 3000000 INFO @ Tue, 02 Aug 2022 13:58:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.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 13:58:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:58:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:58:53: 7000000 INFO @ Tue, 02 Aug 2022 13:58:56: 4000000 INFO @ Tue, 02 Aug 2022 13:58:58: 1000000 INFO @ Tue, 02 Aug 2022 13:59:02: 8000000 INFO @ Tue, 02 Aug 2022 13:59:06: 5000000 INFO @ Tue, 02 Aug 2022 13:59:07: 2000000 INFO @ Tue, 02 Aug 2022 13:59:12: 9000000 INFO @ Tue, 02 Aug 2022 13:59:15: 6000000 INFO @ Tue, 02 Aug 2022 13:59:17: 3000000 INFO @ Tue, 02 Aug 2022 13:59:21: 10000000 INFO @ Tue, 02 Aug 2022 13:59:24: 7000000 INFO @ Tue, 02 Aug 2022 13:59:26: 4000000 INFO @ Tue, 02 Aug 2022 13:59:31: 11000000 INFO @ Tue, 02 Aug 2022 13:59:34: 8000000 INFO @ Tue, 02 Aug 2022 13:59:36: 5000000 INFO @ Tue, 02 Aug 2022 13:59:41: 12000000 INFO @ Tue, 02 Aug 2022 13:59:43: 9000000 INFO @ Tue, 02 Aug 2022 13:59:45: 6000000 INFO @ Tue, 02 Aug 2022 13:59:50: 13000000 INFO @ Tue, 02 Aug 2022 13:59:52: 10000000 INFO @ Tue, 02 Aug 2022 13:59:55: 7000000 INFO @ Tue, 02 Aug 2022 14:00:00: 14000000 INFO @ Tue, 02 Aug 2022 14:00:02: 11000000 INFO @ Tue, 02 Aug 2022 14:00:04: 8000000 INFO @ Tue, 02 Aug 2022 14:00:09: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:00:09: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:00:09: #1 total tags in treatment: 14987397 INFO @ Tue, 02 Aug 2022 14:00:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:00:09: #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 14:00:09: #1 tags after filtering in treatment: 14987397 INFO @ Tue, 02 Aug 2022 14:00:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:00:09: #1 finished! INFO @ Tue, 02 Aug 2022 14:00:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:00:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:00:10: #2 number of paired peaks: 621 WARNING @ Tue, 02 Aug 2022 14:00:10: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Tue, 02 Aug 2022 14:00:10: start model_add_line... INFO @ Tue, 02 Aug 2022 14:00:11: start X-correlation... INFO @ Tue, 02 Aug 2022 14:00:11: end of X-cor INFO @ Tue, 02 Aug 2022 14:00:11: #2 finished! INFO @ Tue, 02 Aug 2022 14:00:11: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 14:00:11: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 14:00:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.05_model.r WARNING @ Tue, 02 Aug 2022 14:00:11: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:00:11: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 14:00:11: #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 14:00:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:00:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:00:12: 12000000 INFO @ Tue, 02 Aug 2022 14:00:14: 9000000 INFO @ Tue, 02 Aug 2022 14:00:20: 13000000 INFO @ Tue, 02 Aug 2022 14:00:23: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:00:29: 14000000 INFO @ Tue, 02 Aug 2022 14:00:32: 11000000 INFO @ Tue, 02 Aug 2022 14:00:38: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:00:38: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:00:38: #1 total tags in treatment: 14987397 INFO @ Tue, 02 Aug 2022 14:00:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:00:38: #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 14:00:38: #1 tags after filtering in treatment: 14987397 INFO @ Tue, 02 Aug 2022 14:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:00:38: #1 finished! INFO @ Tue, 02 Aug 2022 14:00:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:00:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:00:40: #2 number of paired peaks: 621 WARNING @ Tue, 02 Aug 2022 14:00:40: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Tue, 02 Aug 2022 14:00:40: start model_add_line... INFO @ Tue, 02 Aug 2022 14:00:40: start X-correlation... INFO @ Tue, 02 Aug 2022 14:00:40: end of X-cor INFO @ Tue, 02 Aug 2022 14:00:40: #2 finished! INFO @ Tue, 02 Aug 2022 14:00:40: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 14:00:40: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 14:00:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.10_model.r WARNING @ Tue, 02 Aug 2022 14:00:40: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:00:40: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 14:00:40: #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 14:00:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:00:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:00:41: 12000000 INFO @ Tue, 02 Aug 2022 14:00:51: 13000000 INFO @ Tue, 02 Aug 2022 14:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:00:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.05_summits.bed INFO @ Tue, 02 Aug 2022 14:00:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2299 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:01:00: 14000000 INFO @ Tue, 02 Aug 2022 14:01:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:01:09: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:01:09: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:01:09: #1 total tags in treatment: 14987397 INFO @ Tue, 02 Aug 2022 14:01:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:01:09: #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 14:01:09: #1 tags after filtering in treatment: 14987397 INFO @ Tue, 02 Aug 2022 14:01:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:01:09: #1 finished! INFO @ Tue, 02 Aug 2022 14:01:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:01:11: #2 number of paired peaks: 621 WARNING @ Tue, 02 Aug 2022 14:01:11: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Tue, 02 Aug 2022 14:01:11: start model_add_line... INFO @ Tue, 02 Aug 2022 14:01:11: start X-correlation... INFO @ Tue, 02 Aug 2022 14:01:11: end of X-cor INFO @ Tue, 02 Aug 2022 14:01:11: #2 finished! INFO @ Tue, 02 Aug 2022 14:01:11: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 14:01:11: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 14:01:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.20_model.r WARNING @ Tue, 02 Aug 2022 14:01:11: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:01:11: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 14:01:11: #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 14:01:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:01:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:01:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:01:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:01:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.10_summits.bed INFO @ Tue, 02 Aug 2022 14:01:21: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1319 records, 4 fields): 77 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:01:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:01:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:01:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:01:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148468/SRX14148468.20_summits.bed INFO @ Tue, 02 Aug 2022 14:01:52: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (679 records, 4 fields): 17 millis CompletedMACS2peakCalling