Job ID = 16437213 SRX = SRX12119060 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 38680774 spots for SRR15827098/SRR15827098.sra Written 38680774 spots for SRR15827098/SRR15827098.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438143 ("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: 01:15:10 38680774 reads; of these: 38680774 (100.00%) were paired; of these: 26168104 (67.65%) aligned concordantly 0 times 8393538 (21.70%) aligned concordantly exactly 1 time 4119132 (10.65%) aligned concordantly >1 times ---- 26168104 pairs aligned concordantly 0 times; of these: 3570043 (13.64%) aligned discordantly 1 time ---- 22598061 pairs aligned 0 times concordantly or discordantly; of these: 45196122 mates make up the pairs; of these: 40572380 (89.77%) aligned 0 times 1684992 (3.73%) aligned exactly 1 time 2938750 (6.50%) aligned >1 times 47.55% overall alignment rate Time searching: 01:15:10 Overall time: 01:15:10 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] 3533524 / 15994819 = 0.2209 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 13:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.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 13:58:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:58:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:58:36: 1000000 INFO @ Tue, 02 Aug 2022 13:58:44: 2000000 INFO @ Tue, 02 Aug 2022 13:58:51: 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 13:58:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.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 13:58:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:58:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:59:00: 4000000 INFO @ Tue, 02 Aug 2022 13:59:09: 1000000 INFO @ Tue, 02 Aug 2022 13:59:09: 5000000 INFO @ Tue, 02 Aug 2022 13:59:19: 6000000 INFO @ Tue, 02 Aug 2022 13:59:20: 2000000 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 13:59:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.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 13:59:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:59:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:59:28: 7000000 INFO @ Tue, 02 Aug 2022 13:59:32: 3000000 INFO @ Tue, 02 Aug 2022 13:59:38: 1000000 INFO @ Tue, 02 Aug 2022 13:59:39: 8000000 INFO @ Tue, 02 Aug 2022 13:59:43: 4000000 INFO @ Tue, 02 Aug 2022 13:59:48: 2000000 INFO @ Tue, 02 Aug 2022 13:59:49: 9000000 INFO @ Tue, 02 Aug 2022 13:59:55: 5000000 INFO @ Tue, 02 Aug 2022 13:59:58: 3000000 INFO @ Tue, 02 Aug 2022 13:59:59: 10000000 INFO @ Tue, 02 Aug 2022 14:00:06: 6000000 INFO @ Tue, 02 Aug 2022 14:00:09: 4000000 INFO @ Tue, 02 Aug 2022 14:00:09: 11000000 INFO @ Tue, 02 Aug 2022 14:00:17: 7000000 INFO @ Tue, 02 Aug 2022 14:00:19: 5000000 INFO @ Tue, 02 Aug 2022 14:00:19: 12000000 INFO @ Tue, 02 Aug 2022 14:00:29: 8000000 INFO @ Tue, 02 Aug 2022 14:00:29: 6000000 INFO @ Tue, 02 Aug 2022 14:00:30: 13000000 INFO @ Tue, 02 Aug 2022 14:00:39: 7000000 INFO @ Tue, 02 Aug 2022 14:00:40: 14000000 INFO @ Tue, 02 Aug 2022 14:00:40: 9000000 INFO @ Tue, 02 Aug 2022 14:00:49: 8000000 INFO @ Tue, 02 Aug 2022 14:00:50: 15000000 INFO @ Tue, 02 Aug 2022 14:00:51: 10000000 INFO @ Tue, 02 Aug 2022 14:01:00: 9000000 INFO @ Tue, 02 Aug 2022 14:01:00: 16000000 INFO @ Tue, 02 Aug 2022 14:01:03: 11000000 INFO @ Tue, 02 Aug 2022 14:01:10: 10000000 INFO @ Tue, 02 Aug 2022 14:01:10: 17000000 INFO @ Tue, 02 Aug 2022 14:01:15: 12000000 INFO @ Tue, 02 Aug 2022 14:01:20: 11000000 INFO @ Tue, 02 Aug 2022 14:01:20: 18000000 INFO @ Tue, 02 Aug 2022 14:01:26: 13000000 INFO @ Tue, 02 Aug 2022 14:01:30: 19000000 INFO @ Tue, 02 Aug 2022 14:01:30: 12000000 INFO @ Tue, 02 Aug 2022 14:01:38: 14000000 INFO @ Tue, 02 Aug 2022 14:01:40: 20000000 INFO @ Tue, 02 Aug 2022 14:01:41: 13000000 INFO @ Tue, 02 Aug 2022 14:01:49: 15000000 INFO @ Tue, 02 Aug 2022 14:01:50: 21000000 INFO @ Tue, 02 Aug 2022 14:01:51: 14000000 INFO @ Tue, 02 Aug 2022 14:02:00: 22000000 INFO @ Tue, 02 Aug 2022 14:02:01: 16000000 INFO @ Tue, 02 Aug 2022 14:02:01: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:02:09: 23000000 INFO @ Tue, 02 Aug 2022 14:02:11: 16000000 INFO @ Tue, 02 Aug 2022 14:02:12: 17000000 INFO @ Tue, 02 Aug 2022 14:02:19: 24000000 INFO @ Tue, 02 Aug 2022 14:02:21: 17000000 INFO @ Tue, 02 Aug 2022 14:02:23: 18000000 INFO @ Tue, 02 Aug 2022 14:02:29: 25000000 INFO @ Tue, 02 Aug 2022 14:02:31: 18000000 INFO @ Tue, 02 Aug 2022 14:02:35: 19000000 INFO @ Tue, 02 Aug 2022 14:02:39: 26000000 INFO @ Tue, 02 Aug 2022 14:02:41: 19000000 INFO @ Tue, 02 Aug 2022 14:02:46: 20000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:02:50: 27000000 INFO @ Tue, 02 Aug 2022 14:02:51: 20000000 INFO @ Tue, 02 Aug 2022 14:02:57: 21000000 INFO @ Tue, 02 Aug 2022 14:03:00: 28000000 INFO @ Tue, 02 Aug 2022 14:03:01: 21000000 INFO @ Tue, 02 Aug 2022 14:03:08: 22000000 INFO @ Tue, 02 Aug 2022 14:03:10: 29000000 INFO @ Tue, 02 Aug 2022 14:03:11: 22000000 INFO @ Tue, 02 Aug 2022 14:03:17: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:03:17: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:03:17: #1 total tags in treatment: 9433338 INFO @ Tue, 02 Aug 2022 14:03:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:03:17: #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 14:03:17: #1 tags after filtering in treatment: 7211902 INFO @ Tue, 02 Aug 2022 14:03:17: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 14:03:17: #1 finished! INFO @ Tue, 02 Aug 2022 14:03:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:03:18: #2 number of paired peaks: 1590 INFO @ Tue, 02 Aug 2022 14:03:18: start model_add_line... INFO @ Tue, 02 Aug 2022 14:03:18: start X-correlation... INFO @ Tue, 02 Aug 2022 14:03:18: end of X-cor INFO @ Tue, 02 Aug 2022 14:03:18: #2 finished! INFO @ Tue, 02 Aug 2022 14:03:18: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 14:03:18: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 14:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.05_model.r WARNING @ Tue, 02 Aug 2022 14:03:18: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:03:18: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 14:03:18: #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 14:03:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:03:19: 23000000 INFO @ Tue, 02 Aug 2022 14:03:21: 23000000 INFO @ Tue, 02 Aug 2022 14:03:31: 24000000 INFO @ Tue, 02 Aug 2022 14:03:32: 24000000 INFO @ Tue, 02 Aug 2022 14:03:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:03:42: 25000000 INFO @ Tue, 02 Aug 2022 14:03:43: 25000000 INFO @ Tue, 02 Aug 2022 14:03:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.05_summits.bed INFO @ Tue, 02 Aug 2022 14:03:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7360 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:03:53: 26000000 INFO @ Tue, 02 Aug 2022 14:03:54: 26000000 INFO @ Tue, 02 Aug 2022 14:04:05: 27000000 INFO @ Tue, 02 Aug 2022 14:04:06: 27000000 INFO @ Tue, 02 Aug 2022 14:04:16: 28000000 INFO @ Tue, 02 Aug 2022 14:04:17: 28000000 INFO @ Tue, 02 Aug 2022 14:04:28: 29000000 INFO @ Tue, 02 Aug 2022 14:04:28: 29000000 INFO @ Tue, 02 Aug 2022 14:04:37: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:04:37: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:04:37: #1 total tags in treatment: 9433338 INFO @ Tue, 02 Aug 2022 14:04:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:04:37: #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 14:04:37: #1 tags after filtering in treatment: 7211902 INFO @ Tue, 02 Aug 2022 14:04:37: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 14:04:37: #1 finished! INFO @ Tue, 02 Aug 2022 14:04:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:04:37: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:04:37: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:04:37: #1 total tags in treatment: 9433338 INFO @ Tue, 02 Aug 2022 14:04:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:04:37: #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 14:04:37: #1 tags after filtering in treatment: 7211902 INFO @ Tue, 02 Aug 2022 14:04:37: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 14:04:37: #1 finished! INFO @ Tue, 02 Aug 2022 14:04:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:04:38: #2 number of paired peaks: 1590 INFO @ Tue, 02 Aug 2022 14:04:38: start model_add_line... INFO @ Tue, 02 Aug 2022 14:04:38: start X-correlation... INFO @ Tue, 02 Aug 2022 14:04:38: end of X-cor INFO @ Tue, 02 Aug 2022 14:04:38: #2 finished! INFO @ Tue, 02 Aug 2022 14:04:38: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 14:04:38: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 14:04:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.10_model.r WARNING @ Tue, 02 Aug 2022 14:04:38: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:04:38: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 14:04:38: #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 14:04:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:04:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:04:38: #2 number of paired peaks: 1590 INFO @ Tue, 02 Aug 2022 14:04:38: start model_add_line... INFO @ Tue, 02 Aug 2022 14:04:38: start X-correlation... INFO @ Tue, 02 Aug 2022 14:04:38: end of X-cor INFO @ Tue, 02 Aug 2022 14:04:38: #2 finished! INFO @ Tue, 02 Aug 2022 14:04:38: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 14:04:38: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 14:04:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.20_model.r WARNING @ Tue, 02 Aug 2022 14:04:38: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:04:38: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 14:04:38: #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 14:04:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:04:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:04:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:04:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:05:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:05:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.10_summits.bed INFO @ Tue, 02 Aug 2022 14:05:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4459 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:05:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:05:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:05:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119060/SRX12119060.20_summits.bed INFO @ Tue, 02 Aug 2022 14:05:04: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1872 records, 4 fields): 66 millis CompletedMACS2peakCalling