Job ID = 14170622 SRX = SRX9660889 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22899541 spots for SRR13228529/SRR13228529.sra Written 22899541 spots for SRR13228529/SRR13228529.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171202 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:52:30 22899541 reads; of these: 22899541 (100.00%) were paired; of these: 6860247 (29.96%) aligned concordantly 0 times 14127479 (61.69%) aligned concordantly exactly 1 time 1911815 (8.35%) aligned concordantly >1 times ---- 6860247 pairs aligned concordantly 0 times; of these: 1586832 (23.13%) aligned discordantly 1 time ---- 5273415 pairs aligned 0 times concordantly or discordantly; of these: 10546830 mates make up the pairs; of these: 9231248 (87.53%) aligned 0 times 764748 (7.25%) aligned exactly 1 time 550834 (5.22%) aligned >1 times 79.84% overall alignment rate Time searching: 00:52:31 Overall time: 00:52:31 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 28 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2749381 / 16200240 = 0.1697 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 08:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.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 08:44:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:44:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:44:29: 1000000 INFO @ Sat, 11 Dec 2021 08:44:37: 2000000 INFO @ Sat, 11 Dec 2021 08:44:44: 3000000 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 08:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.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 08:44:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:44:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:44:52: 4000000 INFO @ Sat, 11 Dec 2021 08:45:00: 1000000 INFO @ Sat, 11 Dec 2021 08:45:01: 5000000 INFO @ Sat, 11 Dec 2021 08:45:10: 6000000 INFO @ Sat, 11 Dec 2021 08:45:10: 2000000 INFO @ Sat, 11 Dec 2021 08:45:18: 7000000 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 08:45:20: 3000000 INFO @ Sat, 11 Dec 2021 08:45:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.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 08:45:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:45:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:45:27: 8000000 INFO @ Sat, 11 Dec 2021 08:45:29: 4000000 INFO @ Sat, 11 Dec 2021 08:45:31: 1000000 INFO @ Sat, 11 Dec 2021 08:45:37: 9000000 INFO @ Sat, 11 Dec 2021 08:45:38: 5000000 INFO @ Sat, 11 Dec 2021 08:45:41: 2000000 INFO @ Sat, 11 Dec 2021 08:45:46: 10000000 INFO @ Sat, 11 Dec 2021 08:45:48: 6000000 INFO @ Sat, 11 Dec 2021 08:45:50: 3000000 INFO @ Sat, 11 Dec 2021 08:45:55: 11000000 INFO @ Sat, 11 Dec 2021 08:45:57: 7000000 INFO @ Sat, 11 Dec 2021 08:46:00: 4000000 INFO @ Sat, 11 Dec 2021 08:46:04: 12000000 INFO @ Sat, 11 Dec 2021 08:46:06: 8000000 INFO @ Sat, 11 Dec 2021 08:46:09: 5000000 INFO @ Sat, 11 Dec 2021 08:46:13: 13000000 INFO @ Sat, 11 Dec 2021 08:46:16: 9000000 INFO @ Sat, 11 Dec 2021 08:46:19: 6000000 INFO @ Sat, 11 Dec 2021 08:46:22: 14000000 INFO @ Sat, 11 Dec 2021 08:46:25: 10000000 INFO @ Sat, 11 Dec 2021 08:46:29: 7000000 INFO @ Sat, 11 Dec 2021 08:46:31: 15000000 INFO @ Sat, 11 Dec 2021 08:46:34: 11000000 INFO @ Sat, 11 Dec 2021 08:46:38: 8000000 INFO @ Sat, 11 Dec 2021 08:46:41: 16000000 INFO @ Sat, 11 Dec 2021 08:46:43: 12000000 INFO @ Sat, 11 Dec 2021 08:46:48: 9000000 INFO @ Sat, 11 Dec 2021 08:46:50: 17000000 INFO @ Sat, 11 Dec 2021 08:46:52: 13000000 INFO @ Sat, 11 Dec 2021 08:46:57: 10000000 INFO @ Sat, 11 Dec 2021 08:46:59: 18000000 INFO @ Sat, 11 Dec 2021 08:47:02: 14000000 INFO @ Sat, 11 Dec 2021 08:47:06: 11000000 INFO @ Sat, 11 Dec 2021 08:47:08: 19000000 INFO @ Sat, 11 Dec 2021 08:47:11: 15000000 INFO @ Sat, 11 Dec 2021 08:47:15: 12000000 INFO @ Sat, 11 Dec 2021 08:47:17: 20000000 INFO @ Sat, 11 Dec 2021 08:47:20: 16000000 INFO @ Sat, 11 Dec 2021 08:47:25: 13000000 INFO @ Sat, 11 Dec 2021 08:47:26: 21000000 INFO @ Sat, 11 Dec 2021 08:47:29: 17000000 INFO @ Sat, 11 Dec 2021 08:47:34: 14000000 INFO @ Sat, 11 Dec 2021 08:47:36: 22000000 INFO @ Sat, 11 Dec 2021 08:47:38: 18000000 INFO @ Sat, 11 Dec 2021 08:47:43: 15000000 INFO @ Sat, 11 Dec 2021 08:47:45: 23000000 INFO @ Sat, 11 Dec 2021 08:47:48: 19000000 INFO @ Sat, 11 Dec 2021 08:47:52: 16000000 INFO @ Sat, 11 Dec 2021 08:47:54: 24000000 INFO @ Sat, 11 Dec 2021 08:47:57: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:48:01: 17000000 INFO @ Sat, 11 Dec 2021 08:48:03: 25000000 INFO @ Sat, 11 Dec 2021 08:48:06: 21000000 INFO @ Sat, 11 Dec 2021 08:48:11: 18000000 INFO @ Sat, 11 Dec 2021 08:48:12: 26000000 INFO @ Sat, 11 Dec 2021 08:48:15: 22000000 INFO @ Sat, 11 Dec 2021 08:48:20: 19000000 INFO @ Sat, 11 Dec 2021 08:48:21: 27000000 INFO @ Sat, 11 Dec 2021 08:48:24: 23000000 INFO @ Sat, 11 Dec 2021 08:48:29: 20000000 INFO @ Sat, 11 Dec 2021 08:48:31: 28000000 INFO @ Sat, 11 Dec 2021 08:48:33: 24000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:48:39: 21000000 INFO @ Sat, 11 Dec 2021 08:48:40: 29000000 INFO @ Sat, 11 Dec 2021 08:48:43: 25000000 INFO @ Sat, 11 Dec 2021 08:48:48: 22000000 INFO @ Sat, 11 Dec 2021 08:48:49: 30000000 INFO @ Sat, 11 Dec 2021 08:48:52: 26000000 INFO @ Sat, 11 Dec 2021 08:48:58: 31000000 INFO @ Sat, 11 Dec 2021 08:48:58: 23000000 INFO @ Sat, 11 Dec 2021 08:48:58: #1 tag size is determined as 144 bps INFO @ Sat, 11 Dec 2021 08:48:58: #1 tag size = 144 INFO @ Sat, 11 Dec 2021 08:48:58: #1 total tags in treatment: 13465549 INFO @ Sat, 11 Dec 2021 08:48:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:48:58: #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 08:48:59: #1 tags after filtering in treatment: 8669934 INFO @ Sat, 11 Dec 2021 08:48:59: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 11 Dec 2021 08:48:59: #1 finished! INFO @ Sat, 11 Dec 2021 08:48:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:48:59: #2 number of paired peaks: 2896 INFO @ Sat, 11 Dec 2021 08:48:59: start model_add_line... INFO @ Sat, 11 Dec 2021 08:49:00: start X-correlation... INFO @ Sat, 11 Dec 2021 08:49:00: end of X-cor INFO @ Sat, 11 Dec 2021 08:49:00: #2 finished! INFO @ Sat, 11 Dec 2021 08:49:00: #2 predicted fragment length is 264 bps INFO @ Sat, 11 Dec 2021 08:49:00: #2 alternative fragment length(s) may be 264 bps INFO @ Sat, 11 Dec 2021 08:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.05_model.r WARNING @ Sat, 11 Dec 2021 08:49:00: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:49:00: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Sat, 11 Dec 2021 08:49:00: #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 08:49:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:49:01: 27000000 INFO @ Sat, 11 Dec 2021 08:49:07: 24000000 INFO @ Sat, 11 Dec 2021 08:49:10: 28000000 INFO @ Sat, 11 Dec 2021 08:49:16: 25000000 INFO @ Sat, 11 Dec 2021 08:49:19: 29000000 INFO @ Sat, 11 Dec 2021 08:49:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:49:25: 26000000 INFO @ Sat, 11 Dec 2021 08:49:28: 30000000 INFO @ Sat, 11 Dec 2021 08:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.05_summits.bed INFO @ Sat, 11 Dec 2021 08:49:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7534 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:49:34: 27000000 INFO @ Sat, 11 Dec 2021 08:49:37: 31000000 INFO @ Sat, 11 Dec 2021 08:49:37: #1 tag size is determined as 144 bps INFO @ Sat, 11 Dec 2021 08:49:37: #1 tag size = 144 INFO @ Sat, 11 Dec 2021 08:49:37: #1 total tags in treatment: 13465549 INFO @ Sat, 11 Dec 2021 08:49:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:49:37: #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 08:49:38: #1 tags after filtering in treatment: 8669934 INFO @ Sat, 11 Dec 2021 08:49:38: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 11 Dec 2021 08:49:38: #1 finished! INFO @ Sat, 11 Dec 2021 08:49:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:49:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:49:38: #2 number of paired peaks: 2896 INFO @ Sat, 11 Dec 2021 08:49:38: start model_add_line... INFO @ Sat, 11 Dec 2021 08:49:38: start X-correlation... INFO @ Sat, 11 Dec 2021 08:49:38: end of X-cor INFO @ Sat, 11 Dec 2021 08:49:38: #2 finished! INFO @ Sat, 11 Dec 2021 08:49:38: #2 predicted fragment length is 264 bps INFO @ Sat, 11 Dec 2021 08:49:38: #2 alternative fragment length(s) may be 264 bps INFO @ Sat, 11 Dec 2021 08:49:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.10_model.r WARNING @ Sat, 11 Dec 2021 08:49:38: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:49:38: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Sat, 11 Dec 2021 08:49:38: #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 08:49:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:49:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:49:43: 28000000 INFO @ Sat, 11 Dec 2021 08:49:51: 29000000 INFO @ Sat, 11 Dec 2021 08:49:59: 30000000 INFO @ Sat, 11 Dec 2021 08:50:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:50:08: 31000000 INFO @ Sat, 11 Dec 2021 08:50:08: #1 tag size is determined as 144 bps INFO @ Sat, 11 Dec 2021 08:50:08: #1 tag size = 144 INFO @ Sat, 11 Dec 2021 08:50:08: #1 total tags in treatment: 13465549 INFO @ Sat, 11 Dec 2021 08:50:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:50:08: #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 08:50:08: #1 tags after filtering in treatment: 8669934 INFO @ Sat, 11 Dec 2021 08:50:08: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 11 Dec 2021 08:50:08: #1 finished! INFO @ Sat, 11 Dec 2021 08:50:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:50:09: #2 number of paired peaks: 2896 INFO @ Sat, 11 Dec 2021 08:50:09: start model_add_line... INFO @ Sat, 11 Dec 2021 08:50:09: start X-correlation... INFO @ Sat, 11 Dec 2021 08:50:09: end of X-cor INFO @ Sat, 11 Dec 2021 08:50:09: #2 finished! INFO @ Sat, 11 Dec 2021 08:50:09: #2 predicted fragment length is 264 bps INFO @ Sat, 11 Dec 2021 08:50:09: #2 alternative fragment length(s) may be 264 bps INFO @ Sat, 11 Dec 2021 08:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.20_model.r WARNING @ Sat, 11 Dec 2021 08:50:09: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:50:09: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Sat, 11 Dec 2021 08:50:09: #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 08:50:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.10_summits.bed INFO @ Sat, 11 Dec 2021 08:50:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5690 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:50:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9660889/SRX9660889.20_summits.bed INFO @ Sat, 11 Dec 2021 08:50:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3815 records, 4 fields): 6 millis CompletedMACS2peakCalling