Job ID = 16438122 SRX = SRX14148469 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22647565 spots for SRR17992808/SRR17992808.sra Written 22647565 spots for SRR17992808/SRR17992808.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438579 ("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: 00:12:17 22647565 reads; of these: 22647565 (100.00%) were unpaired; of these: 1016305 (4.49%) aligned 0 times 14088337 (62.21%) aligned exactly 1 time 7542923 (33.31%) aligned >1 times 95.51% overall alignment rate Time searching: 00:12:17 Overall time: 00:12:17 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] 3792987 / 21631260 = 0.1753 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 14:03:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.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 14:03:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:03:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:03:19: 1000000 INFO @ Tue, 02 Aug 2022 14:03:25: 2000000 INFO @ Tue, 02 Aug 2022 14:03:31: 3000000 INFO @ Tue, 02 Aug 2022 14:03:38: 4000000 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 14:03:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.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 14:03:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:03:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:03:45: 5000000 INFO @ Tue, 02 Aug 2022 14:03:48: 1000000 INFO @ Tue, 02 Aug 2022 14:03:52: 6000000 INFO @ Tue, 02 Aug 2022 14:03:54: 2000000 INFO @ Tue, 02 Aug 2022 14:03:58: 7000000 INFO @ Tue, 02 Aug 2022 14:04:00: 3000000 INFO @ Tue, 02 Aug 2022 14:04:05: 8000000 INFO @ Tue, 02 Aug 2022 14:04:06: 4000000 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 14:04:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.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 14:04:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:04:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:04:12: 5000000 INFO @ Tue, 02 Aug 2022 14:04:12: 9000000 INFO @ Tue, 02 Aug 2022 14:04:18: 6000000 INFO @ Tue, 02 Aug 2022 14:04:18: 1000000 INFO @ Tue, 02 Aug 2022 14:04:19: 10000000 INFO @ Tue, 02 Aug 2022 14:04:24: 7000000 INFO @ Tue, 02 Aug 2022 14:04:24: 2000000 INFO @ Tue, 02 Aug 2022 14:04:25: 11000000 INFO @ Tue, 02 Aug 2022 14:04:30: 8000000 INFO @ Tue, 02 Aug 2022 14:04:32: 3000000 INFO @ Tue, 02 Aug 2022 14:04:33: 12000000 INFO @ Tue, 02 Aug 2022 14:04:37: 9000000 INFO @ Tue, 02 Aug 2022 14:04:39: 4000000 INFO @ Tue, 02 Aug 2022 14:04:41: 13000000 INFO @ Tue, 02 Aug 2022 14:04:44: 10000000 INFO @ Tue, 02 Aug 2022 14:04:46: 5000000 INFO @ Tue, 02 Aug 2022 14:04:48: 14000000 INFO @ Tue, 02 Aug 2022 14:04:50: 11000000 INFO @ Tue, 02 Aug 2022 14:04:53: 6000000 INFO @ Tue, 02 Aug 2022 14:04:56: 15000000 INFO @ Tue, 02 Aug 2022 14:04:56: 12000000 INFO @ Tue, 02 Aug 2022 14:04:59: 7000000 INFO @ Tue, 02 Aug 2022 14:05:03: 13000000 INFO @ Tue, 02 Aug 2022 14:05:03: 16000000 INFO @ Tue, 02 Aug 2022 14:05:06: 8000000 INFO @ Tue, 02 Aug 2022 14:05:09: 14000000 INFO @ Tue, 02 Aug 2022 14:05:11: 17000000 INFO @ Tue, 02 Aug 2022 14:05:13: 9000000 INFO @ Tue, 02 Aug 2022 14:05:15: 15000000 INFO @ Tue, 02 Aug 2022 14:05:17: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:05:17: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:05:17: #1 total tags in treatment: 17838273 INFO @ Tue, 02 Aug 2022 14:05:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:05:17: #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 14:05:17: #1 tags after filtering in treatment: 17838273 INFO @ Tue, 02 Aug 2022 14:05:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:05:17: #1 finished! INFO @ Tue, 02 Aug 2022 14:05:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:05:18: #2 number of paired peaks: 724 WARNING @ Tue, 02 Aug 2022 14:05:18: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Tue, 02 Aug 2022 14:05:18: start model_add_line... INFO @ Tue, 02 Aug 2022 14:05:19: start X-correlation... INFO @ Tue, 02 Aug 2022 14:05:19: end of X-cor INFO @ Tue, 02 Aug 2022 14:05:19: #2 finished! INFO @ Tue, 02 Aug 2022 14:05:19: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:05:19: #2 alternative fragment length(s) may be 3,81,596 bps INFO @ Tue, 02 Aug 2022 14:05:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.05_model.r WARNING @ Tue, 02 Aug 2022 14:05:19: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:05:19: #2 You may need to consider one of the other alternative d(s): 3,81,596 WARNING @ Tue, 02 Aug 2022 14:05:19: #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 14:05:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:05:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:05:20: 10000000 INFO @ Tue, 02 Aug 2022 14:05:21: 16000000 INFO @ Tue, 02 Aug 2022 14:05:26: 11000000 INFO @ Tue, 02 Aug 2022 14:05:27: 17000000 INFO @ Tue, 02 Aug 2022 14:05:33: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:05:33: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:05:33: #1 total tags in treatment: 17838273 INFO @ Tue, 02 Aug 2022 14:05:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:05:33: #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 14:05:33: #1 tags after filtering in treatment: 17838273 INFO @ Tue, 02 Aug 2022 14:05:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:05:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:05:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:05:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:05:33: 12000000 INFO @ Tue, 02 Aug 2022 14:05:34: #2 number of paired peaks: 724 WARNING @ Tue, 02 Aug 2022 14:05:34: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Tue, 02 Aug 2022 14:05:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:05:35: start X-correlation... INFO @ Tue, 02 Aug 2022 14:05:35: end of X-cor INFO @ Tue, 02 Aug 2022 14:05:35: #2 finished! INFO @ Tue, 02 Aug 2022 14:05:35: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:05:35: #2 alternative fragment length(s) may be 3,81,596 bps INFO @ Tue, 02 Aug 2022 14:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.10_model.r WARNING @ Tue, 02 Aug 2022 14:05:35: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:05:35: #2 You may need to consider one of the other alternative d(s): 3,81,596 WARNING @ Tue, 02 Aug 2022 14:05:35: #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 14:05:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:05:40: 13000000 INFO @ Tue, 02 Aug 2022 14:05:47: 14000000 INFO @ Tue, 02 Aug 2022 14:05:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:05:54: 15000000 INFO @ Tue, 02 Aug 2022 14:06:01: 16000000 INFO @ Tue, 02 Aug 2022 14:06:07: 17000000 INFO @ Tue, 02 Aug 2022 14:06:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:06:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:06:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:06:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.05_summits.bed INFO @ Tue, 02 Aug 2022 14:06:09: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3850 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:06:13: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:06:13: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:06:13: #1 total tags in treatment: 17838273 INFO @ Tue, 02 Aug 2022 14:06:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:06:13: #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 14:06:13: #1 tags after filtering in treatment: 17838273 INFO @ Tue, 02 Aug 2022 14:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:06:13: #1 finished! INFO @ Tue, 02 Aug 2022 14:06:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:06:15: #2 number of paired peaks: 724 WARNING @ Tue, 02 Aug 2022 14:06:15: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Tue, 02 Aug 2022 14:06:15: start model_add_line... INFO @ Tue, 02 Aug 2022 14:06:15: start X-correlation... INFO @ Tue, 02 Aug 2022 14:06:15: end of X-cor INFO @ Tue, 02 Aug 2022 14:06:15: #2 finished! INFO @ Tue, 02 Aug 2022 14:06:15: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:06:15: #2 alternative fragment length(s) may be 3,81,596 bps INFO @ Tue, 02 Aug 2022 14:06:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.20_model.r WARNING @ Tue, 02 Aug 2022 14:06:15: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:06:15: #2 You may need to consider one of the other alternative d(s): 3,81,596 WARNING @ Tue, 02 Aug 2022 14:06:15: #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 14:06:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:06:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:06:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:06:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:06:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.10_summits.bed INFO @ Tue, 02 Aug 2022 14:06:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2156 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:06:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:07:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:07:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:07:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148469/SRX14148469.20_summits.bed INFO @ Tue, 02 Aug 2022 14:07:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1191 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。