Job ID = 16439330 SRX = SRX14232168 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19508512 spots for SRR18080650/SRR18080650.sra Written 19508512 spots for SRR18080650/SRR18080650.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440262 ("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: 02:35:58 19508512 reads; of these: 19508512 (100.00%) were paired; of these: 5749391 (29.47%) aligned concordantly 0 times 9080147 (46.54%) aligned concordantly exactly 1 time 4678974 (23.98%) aligned concordantly >1 times ---- 5749391 pairs aligned concordantly 0 times; of these: 1600925 (27.85%) aligned discordantly 1 time ---- 4148466 pairs aligned 0 times concordantly or discordantly; of these: 8296932 mates make up the pairs; of these: 5986215 (72.15%) aligned 0 times 426544 (5.14%) aligned exactly 1 time 1884173 (22.71%) aligned >1 times 84.66% overall alignment rate Time searching: 02:35:58 Overall time: 02:35:58 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 24 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] 2695239 / 15242294 = 0.1768 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 17:50:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.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 17:50:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:50:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:50:55: 1000000 INFO @ Tue, 02 Aug 2022 17:51:03: 2000000 INFO @ Tue, 02 Aug 2022 17:51:12: 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 17:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.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 17:51:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:51:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:51:20: 4000000 INFO @ Tue, 02 Aug 2022 17:51:25: 1000000 INFO @ Tue, 02 Aug 2022 17:51:30: 5000000 INFO @ Tue, 02 Aug 2022 17:51:35: 2000000 INFO @ Tue, 02 Aug 2022 17:51:39: 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 17:51:45: 3000000 INFO @ Tue, 02 Aug 2022 17:51:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.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 17:51:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:51:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:51:48: 7000000 INFO @ Tue, 02 Aug 2022 17:51:56: 4000000 INFO @ Tue, 02 Aug 2022 17:51:56: 1000000 INFO @ Tue, 02 Aug 2022 17:51:59: 8000000 INFO @ Tue, 02 Aug 2022 17:52:07: 5000000 INFO @ Tue, 02 Aug 2022 17:52:07: 2000000 INFO @ Tue, 02 Aug 2022 17:52:09: 9000000 INFO @ Tue, 02 Aug 2022 17:52:17: 3000000 INFO @ Tue, 02 Aug 2022 17:52:18: 6000000 INFO @ Tue, 02 Aug 2022 17:52:19: 10000000 INFO @ Tue, 02 Aug 2022 17:52:28: 4000000 INFO @ Tue, 02 Aug 2022 17:52:29: 7000000 INFO @ Tue, 02 Aug 2022 17:52:30: 11000000 INFO @ Tue, 02 Aug 2022 17:52:39: 5000000 INFO @ Tue, 02 Aug 2022 17:52:39: 8000000 INFO @ Tue, 02 Aug 2022 17:52:40: 12000000 INFO @ Tue, 02 Aug 2022 17:52:49: 6000000 INFO @ Tue, 02 Aug 2022 17:52:50: 13000000 INFO @ Tue, 02 Aug 2022 17:52:50: 9000000 INFO @ Tue, 02 Aug 2022 17:53:00: 7000000 INFO @ Tue, 02 Aug 2022 17:53:00: 14000000 INFO @ Tue, 02 Aug 2022 17:53:01: 10000000 INFO @ Tue, 02 Aug 2022 17:53:10: 8000000 INFO @ Tue, 02 Aug 2022 17:53:11: 15000000 INFO @ Tue, 02 Aug 2022 17:53:12: 11000000 INFO @ Tue, 02 Aug 2022 17:53:20: 9000000 INFO @ Tue, 02 Aug 2022 17:53:21: 16000000 INFO @ Tue, 02 Aug 2022 17:53:23: 12000000 INFO @ Tue, 02 Aug 2022 17:53:31: 17000000 INFO @ Tue, 02 Aug 2022 17:53:31: 10000000 INFO @ Tue, 02 Aug 2022 17:53:33: 13000000 INFO @ Tue, 02 Aug 2022 17:53:41: 18000000 INFO @ Tue, 02 Aug 2022 17:53:41: 11000000 INFO @ Tue, 02 Aug 2022 17:53:44: 14000000 INFO @ Tue, 02 Aug 2022 17:53:51: 19000000 INFO @ Tue, 02 Aug 2022 17:53:52: 12000000 INFO @ Tue, 02 Aug 2022 17:53:55: 15000000 INFO @ Tue, 02 Aug 2022 17:54:01: 20000000 INFO @ Tue, 02 Aug 2022 17:54:02: 13000000 INFO @ Tue, 02 Aug 2022 17:54:06: 16000000 INFO @ Tue, 02 Aug 2022 17:54:11: 21000000 INFO @ Tue, 02 Aug 2022 17:54:12: 14000000 INFO @ Tue, 02 Aug 2022 17:54:16: 17000000 INFO @ Tue, 02 Aug 2022 17:54:21: 22000000 INFO @ Tue, 02 Aug 2022 17:54:22: 15000000 INFO @ Tue, 02 Aug 2022 17:54:27: 18000000 INFO @ Tue, 02 Aug 2022 17:54:31: 23000000 INFO @ Tue, 02 Aug 2022 17:54:33: 16000000 INFO @ Tue, 02 Aug 2022 17:54:37: 19000000 INFO @ Tue, 02 Aug 2022 17:54:42: 24000000 INFO @ Tue, 02 Aug 2022 17:54:43: 17000000 INFO @ Tue, 02 Aug 2022 17:54:48: 20000000 INFO @ Tue, 02 Aug 2022 17:54:52: 25000000 INFO @ Tue, 02 Aug 2022 17:54:53: 18000000 INFO @ Tue, 02 Aug 2022 17:54:58: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:55:03: 19000000 INFO @ Tue, 02 Aug 2022 17:55:03: 26000000 INFO @ Tue, 02 Aug 2022 17:55:09: 22000000 INFO @ Tue, 02 Aug 2022 17:55:13: 20000000 INFO @ Tue, 02 Aug 2022 17:55:14: 27000000 INFO @ Tue, 02 Aug 2022 17:55:20: 23000000 INFO @ Tue, 02 Aug 2022 17:55:21: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:55:21: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:55:21: #1 total tags in treatment: 11331528 INFO @ Tue, 02 Aug 2022 17:55:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:55:21: #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 17:55:21: #1 tags after filtering in treatment: 9306348 INFO @ Tue, 02 Aug 2022 17:55:21: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 02 Aug 2022 17:55:21: #1 finished! INFO @ Tue, 02 Aug 2022 17:55:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:55:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:55:22: #2 number of paired peaks: 2162 INFO @ Tue, 02 Aug 2022 17:55:22: start model_add_line... INFO @ Tue, 02 Aug 2022 17:55:22: start X-correlation... INFO @ Tue, 02 Aug 2022 17:55:22: end of X-cor INFO @ Tue, 02 Aug 2022 17:55:22: #2 finished! INFO @ Tue, 02 Aug 2022 17:55:22: #2 predicted fragment length is 200 bps INFO @ Tue, 02 Aug 2022 17:55:22: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 02 Aug 2022 17:55:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.05_model.r WARNING @ Tue, 02 Aug 2022 17:55:22: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:55:22: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Tue, 02 Aug 2022 17:55:22: #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 17:55:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:55:23: 21000000 INFO @ Tue, 02 Aug 2022 17:55:30: 24000000 INFO @ Tue, 02 Aug 2022 17:55:32: 22000000 INFO @ Tue, 02 Aug 2022 17:55:39: 25000000 INFO @ Tue, 02 Aug 2022 17:55:41: 23000000 INFO @ Tue, 02 Aug 2022 17:55:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:55:49: 26000000 INFO @ Tue, 02 Aug 2022 17:55:50: 24000000 INFO @ Tue, 02 Aug 2022 17:55:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:55:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:55:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.05_summits.bed INFO @ Tue, 02 Aug 2022 17:55:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4949 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:55:59: 27000000 INFO @ Tue, 02 Aug 2022 17:55:59: 25000000 INFO @ Tue, 02 Aug 2022 17:56:05: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:56:05: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:56:05: #1 total tags in treatment: 11331528 INFO @ Tue, 02 Aug 2022 17:56:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:56:05: #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 17:56:05: #1 tags after filtering in treatment: 9306348 INFO @ Tue, 02 Aug 2022 17:56:05: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 02 Aug 2022 17:56:05: #1 finished! INFO @ Tue, 02 Aug 2022 17:56:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:56:06: #2 number of paired peaks: 2162 INFO @ Tue, 02 Aug 2022 17:56:06: start model_add_line... INFO @ Tue, 02 Aug 2022 17:56:06: start X-correlation... INFO @ Tue, 02 Aug 2022 17:56:06: end of X-cor INFO @ Tue, 02 Aug 2022 17:56:06: #2 finished! INFO @ Tue, 02 Aug 2022 17:56:06: #2 predicted fragment length is 200 bps INFO @ Tue, 02 Aug 2022 17:56:06: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 02 Aug 2022 17:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.10_model.r WARNING @ Tue, 02 Aug 2022 17:56:06: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:56:06: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Tue, 02 Aug 2022 17:56:06: #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 17:56:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:56:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:56:08: 26000000 INFO @ Tue, 02 Aug 2022 17:56:17: 27000000 INFO @ Tue, 02 Aug 2022 17:56:22: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:56:22: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:56:22: #1 total tags in treatment: 11331528 INFO @ Tue, 02 Aug 2022 17:56:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:56:22: #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 17:56:22: #1 tags after filtering in treatment: 9306348 INFO @ Tue, 02 Aug 2022 17:56:22: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 02 Aug 2022 17:56:22: #1 finished! INFO @ Tue, 02 Aug 2022 17:56:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:56:23: #2 number of paired peaks: 2162 INFO @ Tue, 02 Aug 2022 17:56:23: start model_add_line... INFO @ Tue, 02 Aug 2022 17:56:23: start X-correlation... INFO @ Tue, 02 Aug 2022 17:56:23: end of X-cor INFO @ Tue, 02 Aug 2022 17:56:23: #2 finished! INFO @ Tue, 02 Aug 2022 17:56:23: #2 predicted fragment length is 200 bps INFO @ Tue, 02 Aug 2022 17:56:23: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 02 Aug 2022 17:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.20_model.r WARNING @ Tue, 02 Aug 2022 17:56:23: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:56:23: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Tue, 02 Aug 2022 17:56:23: #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 17:56:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:56:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:56:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:56:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:56:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.10_summits.bed INFO @ Tue, 02 Aug 2022 17:56:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3727 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:56:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232168/SRX14232168.20_summits.bed INFO @ Tue, 02 Aug 2022 17:56:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2876 records, 4 fields): 56 millis CompletedMACS2peakCalling