Job ID = 14170379 SRX = SRX8689003 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20435920 spots for SRR12174234/SRR12174234.sra Written 20435920 spots for SRR12174234/SRR12174234.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170799 ("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: 00:08:13 20435920 reads; of these: 20435920 (100.00%) were unpaired; of these: 596348 (2.92%) aligned 0 times 12853836 (62.90%) aligned exactly 1 time 6985736 (34.18%) aligned >1 times 97.08% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 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] 2048006 / 19839572 = 0.1032 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 06:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.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 06:48:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:48:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:48:41: 1000000 INFO @ Sat, 11 Dec 2021 06:48:46: 2000000 INFO @ Sat, 11 Dec 2021 06:48:51: 3000000 INFO @ Sat, 11 Dec 2021 06:48:56: 4000000 INFO @ Sat, 11 Dec 2021 06:49:01: 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 06:49:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.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 06:49:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:49:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:49:06: 6000000 INFO @ Sat, 11 Dec 2021 06:49:11: 1000000 INFO @ Sat, 11 Dec 2021 06:49:11: 7000000 INFO @ Sat, 11 Dec 2021 06:49:16: 2000000 INFO @ Sat, 11 Dec 2021 06:49:16: 8000000 INFO @ Sat, 11 Dec 2021 06:49:21: 3000000 INFO @ Sat, 11 Dec 2021 06:49:21: 9000000 INFO @ Sat, 11 Dec 2021 06:49:26: 4000000 INFO @ Sat, 11 Dec 2021 06:49:27: 10000000 INFO @ Sat, 11 Dec 2021 06:49:31: 5000000 INFO @ Sat, 11 Dec 2021 06:49:32: 11000000 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 06:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.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 06:49:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:49:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:49:37: 6000000 INFO @ Sat, 11 Dec 2021 06:49:37: 12000000 INFO @ Sat, 11 Dec 2021 06:49:42: 1000000 INFO @ Sat, 11 Dec 2021 06:49:42: 7000000 INFO @ Sat, 11 Dec 2021 06:49:42: 13000000 INFO @ Sat, 11 Dec 2021 06:49:47: 8000000 INFO @ Sat, 11 Dec 2021 06:49:48: 14000000 INFO @ Sat, 11 Dec 2021 06:49:48: 2000000 INFO @ Sat, 11 Dec 2021 06:49:53: 9000000 INFO @ Sat, 11 Dec 2021 06:49:53: 15000000 INFO @ Sat, 11 Dec 2021 06:49:55: 3000000 INFO @ Sat, 11 Dec 2021 06:49:58: 10000000 INFO @ Sat, 11 Dec 2021 06:49:59: 16000000 INFO @ Sat, 11 Dec 2021 06:50:01: 4000000 INFO @ Sat, 11 Dec 2021 06:50:04: 11000000 INFO @ Sat, 11 Dec 2021 06:50:04: 17000000 INFO @ Sat, 11 Dec 2021 06:50:07: 5000000 INFO @ Sat, 11 Dec 2021 06:50:09: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:50:09: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:50:09: #1 total tags in treatment: 17791566 INFO @ Sat, 11 Dec 2021 06:50:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:50:09: #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 06:50:09: #1 tags after filtering in treatment: 17791566 INFO @ Sat, 11 Dec 2021 06:50:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:50:09: #1 finished! INFO @ Sat, 11 Dec 2021 06:50:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:50:09: 12000000 INFO @ Sat, 11 Dec 2021 06:50:10: #2 number of paired peaks: 114 WARNING @ Sat, 11 Dec 2021 06:50:10: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sat, 11 Dec 2021 06:50:10: start model_add_line... INFO @ Sat, 11 Dec 2021 06:50:10: start X-correlation... INFO @ Sat, 11 Dec 2021 06:50:10: end of X-cor INFO @ Sat, 11 Dec 2021 06:50:10: #2 finished! INFO @ Sat, 11 Dec 2021 06:50:10: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 06:50:10: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 06:50:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.05_model.r WARNING @ Sat, 11 Dec 2021 06:50:10: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:50:10: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 06:50:10: #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 06:50:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:50:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:50:13: 6000000 INFO @ Sat, 11 Dec 2021 06:50:14: 13000000 INFO @ Sat, 11 Dec 2021 06:50:19: 7000000 INFO @ Sat, 11 Dec 2021 06:50:20: 14000000 INFO @ Sat, 11 Dec 2021 06:50:25: 8000000 INFO @ Sat, 11 Dec 2021 06:50:25: 15000000 INFO @ Sat, 11 Dec 2021 06:50:31: 16000000 INFO @ Sat, 11 Dec 2021 06:50:32: 9000000 INFO @ Sat, 11 Dec 2021 06:50:36: 17000000 INFO @ Sat, 11 Dec 2021 06:50:38: 10000000 INFO @ Sat, 11 Dec 2021 06:50:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:50:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:50:41: #1 total tags in treatment: 17791566 INFO @ Sat, 11 Dec 2021 06:50:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:50:41: #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 06:50:41: #1 tags after filtering in treatment: 17791566 INFO @ Sat, 11 Dec 2021 06:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:50:41: #1 finished! INFO @ Sat, 11 Dec 2021 06:50:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:50:42: #2 number of paired peaks: 114 WARNING @ Sat, 11 Dec 2021 06:50:42: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sat, 11 Dec 2021 06:50:42: start model_add_line... INFO @ Sat, 11 Dec 2021 06:50:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:50:42: start X-correlation... INFO @ Sat, 11 Dec 2021 06:50:42: end of X-cor INFO @ Sat, 11 Dec 2021 06:50:42: #2 finished! INFO @ Sat, 11 Dec 2021 06:50:42: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 06:50:42: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 06:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.10_model.r WARNING @ Sat, 11 Dec 2021 06:50:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:50:42: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 06:50:42: #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 06:50:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:50:44: 11000000 INFO @ Sat, 11 Dec 2021 06:50:50: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:50:56: 13000000 INFO @ Sat, 11 Dec 2021 06:50:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:50:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:50:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.05_summits.bed INFO @ Sat, 11 Dec 2021 06:50:58: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2192 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:51:02: 14000000 INFO @ Sat, 11 Dec 2021 06:51:09: 15000000 INFO @ Sat, 11 Dec 2021 06:51:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:51:15: 16000000 INFO @ Sat, 11 Dec 2021 06:51:21: 17000000 INFO @ Sat, 11 Dec 2021 06:51:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:51:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:51:26: #1 total tags in treatment: 17791566 INFO @ Sat, 11 Dec 2021 06:51:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:51:26: #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 06:51:26: #1 tags after filtering in treatment: 17791566 INFO @ Sat, 11 Dec 2021 06:51:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:51:26: #1 finished! INFO @ Sat, 11 Dec 2021 06:51:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:51:27: #2 number of paired peaks: 114 WARNING @ Sat, 11 Dec 2021 06:51:27: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sat, 11 Dec 2021 06:51:27: start model_add_line... INFO @ Sat, 11 Dec 2021 06:51:27: start X-correlation... INFO @ Sat, 11 Dec 2021 06:51:27: end of X-cor INFO @ Sat, 11 Dec 2021 06:51:27: #2 finished! INFO @ Sat, 11 Dec 2021 06:51:27: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 06:51:27: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 06:51:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.20_model.r WARNING @ Sat, 11 Dec 2021 06:51:27: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:51:27: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 06:51:27: #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 06:51:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:51:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:51:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:51:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:51:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.10_summits.bed INFO @ Sat, 11 Dec 2021 06:51:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1560 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:51:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689003/SRX8689003.20_summits.bed INFO @ Sat, 11 Dec 2021 06:52:15: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1053 records, 4 fields): 3 millis CompletedMACS2peakCalling