Job ID = 16439851 SRX = SRX12175814 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28990395 spots for SRR15884953/SRR15884953.sra Written 28990395 spots for SRR15884953/SRR15884953.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440142 ("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: 00:53:13 28990395 reads; of these: 28990395 (100.00%) were paired; of these: 14801849 (51.06%) aligned concordantly 0 times 12558179 (43.32%) aligned concordantly exactly 1 time 1630367 (5.62%) aligned concordantly >1 times ---- 14801849 pairs aligned concordantly 0 times; of these: 5117764 (34.58%) aligned discordantly 1 time ---- 9684085 pairs aligned 0 times concordantly or discordantly; of these: 19368170 mates make up the pairs; of these: 17019192 (87.87%) aligned 0 times 1236308 (6.38%) aligned exactly 1 time 1112670 (5.74%) aligned >1 times 70.65% overall alignment rate Time searching: 00:53:13 Overall time: 00:53:13 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 32 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] 4174876 / 19228148 = 0.2171 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 17:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.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 17:35:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:35:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:35:50: 1000000 INFO @ Tue, 02 Aug 2022 17:35:59: 2000000 INFO @ Tue, 02 Aug 2022 17:36:07: 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 17:36:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.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 17:36:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:36:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:36:16: 4000000 INFO @ Tue, 02 Aug 2022 17:36:21: 1000000 INFO @ Tue, 02 Aug 2022 17:36:27: 5000000 INFO @ Tue, 02 Aug 2022 17:36:31: 2000000 INFO @ Tue, 02 Aug 2022 17:36:37: 6000000 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 17:36:40: 3000000 INFO @ Tue, 02 Aug 2022 17:36:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.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 17:36:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:36:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:36:48: 7000000 INFO @ Tue, 02 Aug 2022 17:36:50: 4000000 INFO @ Tue, 02 Aug 2022 17:36:51: 1000000 INFO @ Tue, 02 Aug 2022 17:36:59: 8000000 INFO @ Tue, 02 Aug 2022 17:37:01: 5000000 INFO @ Tue, 02 Aug 2022 17:37:01: 2000000 INFO @ Tue, 02 Aug 2022 17:37:09: 9000000 INFO @ Tue, 02 Aug 2022 17:37:11: 6000000 INFO @ Tue, 02 Aug 2022 17:37:11: 3000000 INFO @ Tue, 02 Aug 2022 17:37:20: 10000000 INFO @ Tue, 02 Aug 2022 17:37:21: 4000000 INFO @ Tue, 02 Aug 2022 17:37:21: 7000000 INFO @ Tue, 02 Aug 2022 17:37:31: 5000000 INFO @ Tue, 02 Aug 2022 17:37:31: 8000000 INFO @ Tue, 02 Aug 2022 17:37:31: 11000000 INFO @ Tue, 02 Aug 2022 17:37:41: 6000000 INFO @ Tue, 02 Aug 2022 17:37:41: 9000000 INFO @ Tue, 02 Aug 2022 17:37:42: 12000000 INFO @ Tue, 02 Aug 2022 17:37:50: 7000000 INFO @ Tue, 02 Aug 2022 17:37:51: 10000000 INFO @ Tue, 02 Aug 2022 17:37:53: 13000000 INFO @ Tue, 02 Aug 2022 17:38:00: 8000000 INFO @ Tue, 02 Aug 2022 17:38:01: 11000000 INFO @ Tue, 02 Aug 2022 17:38:04: 14000000 INFO @ Tue, 02 Aug 2022 17:38:10: 9000000 INFO @ Tue, 02 Aug 2022 17:38:12: 12000000 INFO @ Tue, 02 Aug 2022 17:38:14: 15000000 INFO @ Tue, 02 Aug 2022 17:38:19: 10000000 INFO @ Tue, 02 Aug 2022 17:38:23: 13000000 INFO @ Tue, 02 Aug 2022 17:38:25: 16000000 INFO @ Tue, 02 Aug 2022 17:38:29: 11000000 INFO @ Tue, 02 Aug 2022 17:38:33: 14000000 INFO @ Tue, 02 Aug 2022 17:38:36: 17000000 INFO @ Tue, 02 Aug 2022 17:38:40: 12000000 INFO @ Tue, 02 Aug 2022 17:38:44: 15000000 INFO @ Tue, 02 Aug 2022 17:38:46: 18000000 INFO @ Tue, 02 Aug 2022 17:38:50: 13000000 INFO @ Tue, 02 Aug 2022 17:38:55: 16000000 INFO @ Tue, 02 Aug 2022 17:38:56: 19000000 INFO @ Tue, 02 Aug 2022 17:39:01: 14000000 INFO @ Tue, 02 Aug 2022 17:39:05: 17000000 INFO @ Tue, 02 Aug 2022 17:39:06: 20000000 INFO @ Tue, 02 Aug 2022 17:39:11: 15000000 INFO @ Tue, 02 Aug 2022 17:39:15: 18000000 INFO @ Tue, 02 Aug 2022 17:39:16: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:39:22: 16000000 INFO @ Tue, 02 Aug 2022 17:39:26: 19000000 INFO @ Tue, 02 Aug 2022 17:39:27: 22000000 INFO @ Tue, 02 Aug 2022 17:39:33: 17000000 INFO @ Tue, 02 Aug 2022 17:39:37: 20000000 INFO @ Tue, 02 Aug 2022 17:39:38: 23000000 INFO @ Tue, 02 Aug 2022 17:39:44: 18000000 INFO @ Tue, 02 Aug 2022 17:39:47: 21000000 INFO @ Tue, 02 Aug 2022 17:39:48: 24000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:39:54: 19000000 INFO @ Tue, 02 Aug 2022 17:39:58: 22000000 INFO @ Tue, 02 Aug 2022 17:39:59: 25000000 INFO @ Tue, 02 Aug 2022 17:40:04: 20000000 INFO @ Tue, 02 Aug 2022 17:40:08: 23000000 INFO @ Tue, 02 Aug 2022 17:40:09: 26000000 INFO @ Tue, 02 Aug 2022 17:40:15: 21000000 INFO @ Tue, 02 Aug 2022 17:40:19: 24000000 INFO @ Tue, 02 Aug 2022 17:40:20: 27000000 INFO @ Tue, 02 Aug 2022 17:40:25: 22000000 INFO @ Tue, 02 Aug 2022 17:40:29: 25000000 INFO @ Tue, 02 Aug 2022 17:40:30: 28000000 INFO @ Tue, 02 Aug 2022 17:40:35: 23000000 INFO @ Tue, 02 Aug 2022 17:40:39: 26000000 INFO @ Tue, 02 Aug 2022 17:40:40: 29000000 INFO @ Tue, 02 Aug 2022 17:40:45: 24000000 INFO @ Tue, 02 Aug 2022 17:40:53: 27000000 INFO @ Tue, 02 Aug 2022 17:40:54: 30000000 INFO @ Tue, 02 Aug 2022 17:40:59: 25000000 INFO @ Tue, 02 Aug 2022 17:41:04: 28000000 INFO @ Tue, 02 Aug 2022 17:41:05: 31000000 INFO @ Tue, 02 Aug 2022 17:41:10: 26000000 INFO @ Tue, 02 Aug 2022 17:41:15: 29000000 INFO @ Tue, 02 Aug 2022 17:41:15: 32000000 INFO @ Tue, 02 Aug 2022 17:41:21: 27000000 INFO @ Tue, 02 Aug 2022 17:41:22: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:41:22: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:41:22: #1 total tags in treatment: 10874618 INFO @ Tue, 02 Aug 2022 17:41:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:41:22: #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 17:41:22: #1 tags after filtering in treatment: 6386488 INFO @ Tue, 02 Aug 2022 17:41:22: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 02 Aug 2022 17:41:22: #1 finished! INFO @ Tue, 02 Aug 2022 17:41:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:41:23: #2 number of paired peaks: 6811 INFO @ Tue, 02 Aug 2022 17:41:23: start model_add_line... INFO @ Tue, 02 Aug 2022 17:41:23: start X-correlation... INFO @ Tue, 02 Aug 2022 17:41:23: end of X-cor INFO @ Tue, 02 Aug 2022 17:41:23: #2 finished! INFO @ Tue, 02 Aug 2022 17:41:23: #2 predicted fragment length is 249 bps INFO @ Tue, 02 Aug 2022 17:41:23: #2 alternative fragment length(s) may be 249 bps INFO @ Tue, 02 Aug 2022 17:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.05_model.r WARNING @ Tue, 02 Aug 2022 17:41:23: #2 Since the d (249) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:41:23: #2 You may need to consider one of the other alternative d(s): 249 WARNING @ Tue, 02 Aug 2022 17:41:23: #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 17:41:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:41:26: 30000000 INFO @ Tue, 02 Aug 2022 17:41:32: 28000000 INFO @ Tue, 02 Aug 2022 17:41:36: 31000000 INFO @ Tue, 02 Aug 2022 17:41:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:41:42: 29000000 INFO @ Tue, 02 Aug 2022 17:41:46: 32000000 INFO @ Tue, 02 Aug 2022 17:41:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:41:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:41:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.05_summits.bed INFO @ Tue, 02 Aug 2022 17:41:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9514 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:41:52: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:41:52: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:41:52: #1 total tags in treatment: 10874618 INFO @ Tue, 02 Aug 2022 17:41:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:41:52: #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 17:41:52: #1 tags after filtering in treatment: 6386488 INFO @ Tue, 02 Aug 2022 17:41:52: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 02 Aug 2022 17:41:52: #1 finished! INFO @ Tue, 02 Aug 2022 17:41:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:41:53: 30000000 INFO @ Tue, 02 Aug 2022 17:41:53: #2 number of paired peaks: 6811 INFO @ Tue, 02 Aug 2022 17:41:53: start model_add_line... INFO @ Tue, 02 Aug 2022 17:41:53: start X-correlation... INFO @ Tue, 02 Aug 2022 17:41:53: end of X-cor INFO @ Tue, 02 Aug 2022 17:41:53: #2 finished! INFO @ Tue, 02 Aug 2022 17:41:53: #2 predicted fragment length is 249 bps INFO @ Tue, 02 Aug 2022 17:41:53: #2 alternative fragment length(s) may be 249 bps INFO @ Tue, 02 Aug 2022 17:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.10_model.r WARNING @ Tue, 02 Aug 2022 17:41:53: #2 Since the d (249) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:41:53: #2 You may need to consider one of the other alternative d(s): 249 WARNING @ Tue, 02 Aug 2022 17:41:53: #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 17:41:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:42:02: 31000000 INFO @ Tue, 02 Aug 2022 17:42:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:42:11: 32000000 INFO @ Tue, 02 Aug 2022 17:42:16: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:42:16: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:42:16: #1 total tags in treatment: 10874618 INFO @ Tue, 02 Aug 2022 17:42:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:42:16: #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 17:42:16: #1 tags after filtering in treatment: 6386488 INFO @ Tue, 02 Aug 2022 17:42:16: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 02 Aug 2022 17:42:16: #1 finished! INFO @ Tue, 02 Aug 2022 17:42:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:42:17: #2 number of paired peaks: 6811 INFO @ Tue, 02 Aug 2022 17:42:17: start model_add_line... INFO @ Tue, 02 Aug 2022 17:42:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:42:17: start X-correlation... INFO @ Tue, 02 Aug 2022 17:42:17: end of X-cor INFO @ Tue, 02 Aug 2022 17:42:17: #2 finished! INFO @ Tue, 02 Aug 2022 17:42:17: #2 predicted fragment length is 249 bps INFO @ Tue, 02 Aug 2022 17:42:17: #2 alternative fragment length(s) may be 249 bps INFO @ Tue, 02 Aug 2022 17:42:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.20_model.r INFO @ Tue, 02 Aug 2022 17:42:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:42:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.10_summits.bed WARNING @ Tue, 02 Aug 2022 17:42:17: #2 Since the d (249) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:42:17: #2 You may need to consider one of the other alternative d(s): 249 WARNING @ Tue, 02 Aug 2022 17:42:17: #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 17:42:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:42:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:42:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7097 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:42:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:42:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:42:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:42:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175814/SRX12175814.20_summits.bed INFO @ Tue, 02 Aug 2022 17:42:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4526 records, 4 fields): 37 millis CompletedMACS2peakCalling