Job ID = 16437337 SRX = SRX12119067 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 38396951 spots for SRR15827105/SRR15827105.sra Written 38396951 spots for SRR15827105/SRR15827105.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438204 ("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: 01:14:06 38396951 reads; of these: 38396951 (100.00%) were paired; of these: 23075588 (60.10%) aligned concordantly 0 times 12773593 (33.27%) aligned concordantly exactly 1 time 2547770 (6.64%) aligned concordantly >1 times ---- 23075588 pairs aligned concordantly 0 times; of these: 5825639 (25.25%) aligned discordantly 1 time ---- 17249949 pairs aligned 0 times concordantly or discordantly; of these: 34499898 mates make up the pairs; of these: 29397915 (85.21%) aligned 0 times 3185106 (9.23%) aligned exactly 1 time 1916877 (5.56%) aligned >1 times 61.72% overall alignment rate Time searching: 01:14:06 Overall time: 01:14:06 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 36 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] 4032027 / 21063382 = 0.1914 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 14:07:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.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 14:07:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:07:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:07:46: 1000000 INFO @ Tue, 02 Aug 2022 14:07:55: 2000000 INFO @ Tue, 02 Aug 2022 14:08:03: 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 14:08:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.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 14:08:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:08:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:08:12: 4000000 INFO @ Tue, 02 Aug 2022 14:08:16: 1000000 INFO @ Tue, 02 Aug 2022 14:08:21: 5000000 INFO @ Tue, 02 Aug 2022 14:08:25: 2000000 INFO @ Tue, 02 Aug 2022 14:08:29: 6000000 INFO @ Tue, 02 Aug 2022 14:08:35: 3000000 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 14:08:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.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 14:08:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:08:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:08:39: 7000000 INFO @ Tue, 02 Aug 2022 14:08:44: 4000000 INFO @ Tue, 02 Aug 2022 14:08:46: 1000000 INFO @ Tue, 02 Aug 2022 14:08:47: 8000000 INFO @ Tue, 02 Aug 2022 14:08:53: 5000000 INFO @ Tue, 02 Aug 2022 14:08:56: 2000000 INFO @ Tue, 02 Aug 2022 14:08:56: 9000000 INFO @ Tue, 02 Aug 2022 14:09:03: 6000000 INFO @ Tue, 02 Aug 2022 14:09:05: 10000000 INFO @ Tue, 02 Aug 2022 14:09:05: 3000000 INFO @ Tue, 02 Aug 2022 14:09:12: 7000000 INFO @ Tue, 02 Aug 2022 14:09:13: 11000000 INFO @ Tue, 02 Aug 2022 14:09:14: 4000000 INFO @ Tue, 02 Aug 2022 14:09:22: 8000000 INFO @ Tue, 02 Aug 2022 14:09:22: 12000000 INFO @ Tue, 02 Aug 2022 14:09:24: 5000000 INFO @ Tue, 02 Aug 2022 14:09:31: 9000000 INFO @ Tue, 02 Aug 2022 14:09:31: 13000000 INFO @ Tue, 02 Aug 2022 14:09:34: 6000000 INFO @ Tue, 02 Aug 2022 14:09:40: 14000000 INFO @ Tue, 02 Aug 2022 14:09:41: 10000000 INFO @ Tue, 02 Aug 2022 14:09:43: 7000000 INFO @ Tue, 02 Aug 2022 14:09:49: 15000000 INFO @ Tue, 02 Aug 2022 14:09:51: 11000000 INFO @ Tue, 02 Aug 2022 14:09:53: 8000000 INFO @ Tue, 02 Aug 2022 14:09:58: 16000000 INFO @ Tue, 02 Aug 2022 14:10:01: 12000000 INFO @ Tue, 02 Aug 2022 14:10:03: 9000000 INFO @ Tue, 02 Aug 2022 14:10:07: 17000000 INFO @ Tue, 02 Aug 2022 14:10:11: 13000000 INFO @ Tue, 02 Aug 2022 14:10:12: 10000000 INFO @ Tue, 02 Aug 2022 14:10:16: 18000000 INFO @ Tue, 02 Aug 2022 14:10:21: 14000000 INFO @ Tue, 02 Aug 2022 14:10:22: 11000000 INFO @ Tue, 02 Aug 2022 14:10:24: 19000000 INFO @ Tue, 02 Aug 2022 14:10:31: 15000000 INFO @ Tue, 02 Aug 2022 14:10:32: 12000000 INFO @ Tue, 02 Aug 2022 14:10:33: 20000000 INFO @ Tue, 02 Aug 2022 14:10:40: 16000000 INFO @ Tue, 02 Aug 2022 14:10:41: 21000000 INFO @ Tue, 02 Aug 2022 14:10:41: 13000000 INFO @ Tue, 02 Aug 2022 14:10:50: 22000000 INFO @ Tue, 02 Aug 2022 14:10:50: 17000000 INFO @ Tue, 02 Aug 2022 14:10:51: 14000000 INFO @ Tue, 02 Aug 2022 14:10:58: 23000000 INFO @ Tue, 02 Aug 2022 14:10:59: 18000000 INFO @ Tue, 02 Aug 2022 14:11:00: 15000000 INFO @ Tue, 02 Aug 2022 14:11:07: 24000000 INFO @ Tue, 02 Aug 2022 14:11:08: 19000000 INFO @ Tue, 02 Aug 2022 14:11:10: 16000000 INFO @ Tue, 02 Aug 2022 14:11:16: 25000000 INFO @ Tue, 02 Aug 2022 14:11:18: 20000000 INFO @ Tue, 02 Aug 2022 14:11:19: 17000000 INFO @ Tue, 02 Aug 2022 14:11:26: 26000000 INFO @ Tue, 02 Aug 2022 14:11:27: 21000000 INFO @ Tue, 02 Aug 2022 14:11:28: 18000000 INFO @ Tue, 02 Aug 2022 14:11:36: 27000000 INFO @ Tue, 02 Aug 2022 14:11:36: 22000000 INFO @ Tue, 02 Aug 2022 14:11:37: 19000000 INFO @ Tue, 02 Aug 2022 14:11:45: 23000000 INFO @ Tue, 02 Aug 2022 14:11:45: 28000000 INFO @ Tue, 02 Aug 2022 14:11:46: 20000000 INFO @ Tue, 02 Aug 2022 14:11:54: 24000000 INFO @ Tue, 02 Aug 2022 14:11:55: 29000000 INFO @ Tue, 02 Aug 2022 14:11:55: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:12:03: 25000000 INFO @ Tue, 02 Aug 2022 14:12:04: 30000000 INFO @ Tue, 02 Aug 2022 14:12:04: 22000000 INFO @ Tue, 02 Aug 2022 14:12:11: 26000000 INFO @ Tue, 02 Aug 2022 14:12:13: 23000000 INFO @ Tue, 02 Aug 2022 14:12:13: 31000000 INFO @ Tue, 02 Aug 2022 14:12:20: 27000000 INFO @ Tue, 02 Aug 2022 14:12:22: 24000000 INFO @ Tue, 02 Aug 2022 14:12:23: 32000000 INFO @ Tue, 02 Aug 2022 14:12:29: 28000000 INFO @ Tue, 02 Aug 2022 14:12:30: 25000000 INFO @ Tue, 02 Aug 2022 14:12:33: 33000000 INFO @ Tue, 02 Aug 2022 14:12:37: 29000000 INFO @ Tue, 02 Aug 2022 14:12:39: 26000000 INFO @ Tue, 02 Aug 2022 14:12:42: 34000000 INFO @ Tue, 02 Aug 2022 14:12:46: 30000000 INFO @ Tue, 02 Aug 2022 14:12:48: 27000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:12:51: 35000000 INFO @ Tue, 02 Aug 2022 14:12:55: 31000000 INFO @ Tue, 02 Aug 2022 14:12:56: 28000000 INFO @ Tue, 02 Aug 2022 14:13:00: 36000000 INFO @ Tue, 02 Aug 2022 14:13:03: 32000000 INFO @ Tue, 02 Aug 2022 14:13:05: 29000000 INFO @ Tue, 02 Aug 2022 14:13:09: 37000000 INFO @ Tue, 02 Aug 2022 14:13:12: 33000000 INFO @ Tue, 02 Aug 2022 14:13:13: 30000000 INFO @ Tue, 02 Aug 2022 14:13:18: 38000000 INFO @ Tue, 02 Aug 2022 14:13:20: 34000000 INFO @ Tue, 02 Aug 2022 14:13:21: 31000000 INFO @ Tue, 02 Aug 2022 14:13:26: 39000000 INFO @ Tue, 02 Aug 2022 14:13:29: 35000000 INFO @ Tue, 02 Aug 2022 14:13:29: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:13:29: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:13:29: #1 total tags in treatment: 12221347 INFO @ Tue, 02 Aug 2022 14:13:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:13:29: #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 14:13:30: #1 tags after filtering in treatment: 8140393 INFO @ Tue, 02 Aug 2022 14:13:30: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 02 Aug 2022 14:13:30: #1 finished! INFO @ Tue, 02 Aug 2022 14:13:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:13:30: 32000000 INFO @ Tue, 02 Aug 2022 14:13:30: #2 number of paired peaks: 3851 INFO @ Tue, 02 Aug 2022 14:13:30: start model_add_line... INFO @ Tue, 02 Aug 2022 14:13:31: start X-correlation... INFO @ Tue, 02 Aug 2022 14:13:31: end of X-cor INFO @ Tue, 02 Aug 2022 14:13:31: #2 finished! INFO @ Tue, 02 Aug 2022 14:13:31: #2 predicted fragment length is 237 bps INFO @ Tue, 02 Aug 2022 14:13:31: #2 alternative fragment length(s) may be 237 bps INFO @ Tue, 02 Aug 2022 14:13:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.05_model.r WARNING @ Tue, 02 Aug 2022 14:13:31: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:13:31: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Tue, 02 Aug 2022 14:13:31: #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 14:13:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:13:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:13:38: 36000000 INFO @ Tue, 02 Aug 2022 14:13:39: 33000000 INFO @ Tue, 02 Aug 2022 14:13:47: 37000000 INFO @ Tue, 02 Aug 2022 14:13:48: 34000000 INFO @ Tue, 02 Aug 2022 14:13:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:13:56: 38000000 INFO @ Tue, 02 Aug 2022 14:13:57: 35000000 INFO @ Tue, 02 Aug 2022 14:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.05_summits.bed INFO @ Tue, 02 Aug 2022 14:14:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8102 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:14:05: 39000000 INFO @ Tue, 02 Aug 2022 14:14:05: 36000000 INFO @ Tue, 02 Aug 2022 14:14:08: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:14:08: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:14:08: #1 total tags in treatment: 12221347 INFO @ Tue, 02 Aug 2022 14:14:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:14:08: #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 14:14:08: #1 tags after filtering in treatment: 8140393 INFO @ Tue, 02 Aug 2022 14:14:08: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 02 Aug 2022 14:14:08: #1 finished! INFO @ Tue, 02 Aug 2022 14:14:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:14:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:14:09: #2 number of paired peaks: 3851 INFO @ Tue, 02 Aug 2022 14:14:09: start model_add_line... INFO @ Tue, 02 Aug 2022 14:14:09: start X-correlation... INFO @ Tue, 02 Aug 2022 14:14:09: end of X-cor INFO @ Tue, 02 Aug 2022 14:14:09: #2 finished! INFO @ Tue, 02 Aug 2022 14:14:09: #2 predicted fragment length is 237 bps INFO @ Tue, 02 Aug 2022 14:14:09: #2 alternative fragment length(s) may be 237 bps INFO @ Tue, 02 Aug 2022 14:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.10_model.r WARNING @ Tue, 02 Aug 2022 14:14:09: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:14:09: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Tue, 02 Aug 2022 14:14:09: #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 14:14:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:14:13: 37000000 INFO @ Tue, 02 Aug 2022 14:14:21: 38000000 INFO @ Tue, 02 Aug 2022 14:14:28: 39000000 INFO @ Tue, 02 Aug 2022 14:14:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:14:31: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:14:31: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:14:31: #1 total tags in treatment: 12221347 INFO @ Tue, 02 Aug 2022 14:14:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:14:31: #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 14:14:31: #1 tags after filtering in treatment: 8140393 INFO @ Tue, 02 Aug 2022 14:14:31: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 02 Aug 2022 14:14:31: #1 finished! INFO @ Tue, 02 Aug 2022 14:14:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:14:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:14:32: #2 number of paired peaks: 3851 INFO @ Tue, 02 Aug 2022 14:14:32: start model_add_line... INFO @ Tue, 02 Aug 2022 14:14:32: start X-correlation... INFO @ Tue, 02 Aug 2022 14:14:32: end of X-cor INFO @ Tue, 02 Aug 2022 14:14:32: #2 finished! INFO @ Tue, 02 Aug 2022 14:14:32: #2 predicted fragment length is 237 bps INFO @ Tue, 02 Aug 2022 14:14:32: #2 alternative fragment length(s) may be 237 bps INFO @ Tue, 02 Aug 2022 14:14:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.20_model.r WARNING @ Tue, 02 Aug 2022 14:14:32: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:14:32: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Tue, 02 Aug 2022 14:14:32: #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 14:14:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:14:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:14:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:14:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:14:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.10_summits.bed INFO @ Tue, 02 Aug 2022 14:14:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5897 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:14:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119067/SRX12119067.20_summits.bed INFO @ Tue, 02 Aug 2022 14:15:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3604 records, 4 fields): 91 millis CompletedMACS2peakCalling