Job ID = 16439704 SRX = SRX11499371 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19036139 spots for SRR15192730/SRR15192730.sra Written 19036139 spots for SRR15192730/SRR15192730.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440087 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:53:19 19036139 reads; of these: 19036139 (100.00%) were paired; of these: 5553947 (29.18%) aligned concordantly 0 times 11691636 (61.42%) aligned concordantly exactly 1 time 1790556 (9.41%) aligned concordantly >1 times ---- 5553947 pairs aligned concordantly 0 times; of these: 966092 (17.39%) aligned discordantly 1 time ---- 4587855 pairs aligned 0 times concordantly or discordantly; of these: 9175710 mates make up the pairs; of these: 8442358 (92.01%) aligned 0 times 449603 (4.90%) aligned exactly 1 time 283749 (3.09%) aligned >1 times 77.83% overall alignment rate Time searching: 00:53:20 Overall time: 00:53:20 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] 2355574 / 13115345 = 0.1796 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 17:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.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 17:12:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:12:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:13:11: 1000000 INFO @ Tue, 02 Aug 2022 17:13:25: 2000000 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 17:13:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.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 17:13:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:13:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:13:35: 3000000 INFO @ Tue, 02 Aug 2022 17:13:41: 1000000 INFO @ Tue, 02 Aug 2022 17:13:46: 4000000 INFO @ Tue, 02 Aug 2022 17:13:52: 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 17:13:58: 5000000 INFO @ Tue, 02 Aug 2022 17:13:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.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 17:13:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:13:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:14:03: 3000000 INFO @ Tue, 02 Aug 2022 17:14:11: 6000000 INFO @ Tue, 02 Aug 2022 17:14:13: 1000000 INFO @ Tue, 02 Aug 2022 17:14:15: 4000000 INFO @ Tue, 02 Aug 2022 17:14:25: 7000000 INFO @ Tue, 02 Aug 2022 17:14:25: 5000000 INFO @ Tue, 02 Aug 2022 17:14:28: 2000000 INFO @ Tue, 02 Aug 2022 17:14:37: 6000000 INFO @ Tue, 02 Aug 2022 17:14:38: 8000000 INFO @ Tue, 02 Aug 2022 17:14:42: 3000000 INFO @ Tue, 02 Aug 2022 17:14:49: 7000000 INFO @ Tue, 02 Aug 2022 17:14:51: 9000000 INFO @ Tue, 02 Aug 2022 17:14:56: 4000000 INFO @ Tue, 02 Aug 2022 17:15:00: 8000000 INFO @ Tue, 02 Aug 2022 17:15:03: 10000000 INFO @ Tue, 02 Aug 2022 17:15:09: 5000000 INFO @ Tue, 02 Aug 2022 17:15:10: 9000000 INFO @ Tue, 02 Aug 2022 17:15:17: 11000000 INFO @ Tue, 02 Aug 2022 17:15:21: 10000000 INFO @ Tue, 02 Aug 2022 17:15:23: 6000000 INFO @ Tue, 02 Aug 2022 17:15:29: 12000000 INFO @ Tue, 02 Aug 2022 17:15:32: 11000000 INFO @ Tue, 02 Aug 2022 17:15:36: 7000000 INFO @ Tue, 02 Aug 2022 17:15:42: 13000000 INFO @ Tue, 02 Aug 2022 17:15:43: 12000000 INFO @ Tue, 02 Aug 2022 17:15:51: 8000000 INFO @ Tue, 02 Aug 2022 17:15:54: 13000000 INFO @ Tue, 02 Aug 2022 17:15:55: 14000000 INFO @ Tue, 02 Aug 2022 17:16:05: 9000000 INFO @ Tue, 02 Aug 2022 17:16:06: 14000000 INFO @ Tue, 02 Aug 2022 17:16:07: 15000000 INFO @ Tue, 02 Aug 2022 17:16:17: 15000000 INFO @ Tue, 02 Aug 2022 17:16:19: 10000000 INFO @ Tue, 02 Aug 2022 17:16:19: 16000000 INFO @ Tue, 02 Aug 2022 17:16:29: 16000000 INFO @ Tue, 02 Aug 2022 17:16:32: 17000000 INFO @ Tue, 02 Aug 2022 17:16:32: 11000000 INFO @ Tue, 02 Aug 2022 17:16:43: 17000000 INFO @ Tue, 02 Aug 2022 17:16:44: 18000000 INFO @ Tue, 02 Aug 2022 17:16:46: 12000000 INFO @ Tue, 02 Aug 2022 17:16:53: 18000000 INFO @ Tue, 02 Aug 2022 17:16:56: 19000000 INFO @ Tue, 02 Aug 2022 17:17:00: 13000000 INFO @ Tue, 02 Aug 2022 17:17:04: 19000000 INFO @ Tue, 02 Aug 2022 17:17:08: 20000000 INFO @ Tue, 02 Aug 2022 17:17:14: 14000000 INFO @ Tue, 02 Aug 2022 17:17:15: 20000000 INFO @ Tue, 02 Aug 2022 17:17:22: 21000000 INFO @ Tue, 02 Aug 2022 17:17:26: 21000000 INFO @ Tue, 02 Aug 2022 17:17:28: 15000000 INFO @ Tue, 02 Aug 2022 17:17:35: 22000000 INFO @ Tue, 02 Aug 2022 17:17:37: 22000000 INFO @ Tue, 02 Aug 2022 17:17:42: 16000000 INFO @ Tue, 02 Aug 2022 17:17:48: 23000000 INFO @ Tue, 02 Aug 2022 17:17:49: 23000000 INFO @ Tue, 02 Aug 2022 17:17:57: 17000000 INFO @ Tue, 02 Aug 2022 17:18:00: 24000000 INFO @ Tue, 02 Aug 2022 17:18:00: 24000000 INFO @ Tue, 02 Aug 2022 17:18:10: #1 tag size is determined as 144 bps INFO @ Tue, 02 Aug 2022 17:18:10: #1 tag size = 144 INFO @ Tue, 02 Aug 2022 17:18:10: #1 total tags in treatment: 11241637 INFO @ Tue, 02 Aug 2022 17:18:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:18:10: #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 17:18:10: #1 tags after filtering in treatment: 9967407 INFO @ Tue, 02 Aug 2022 17:18:10: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 02 Aug 2022 17:18:10: #1 finished! INFO @ Tue, 02 Aug 2022 17:18:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:18:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:18:11: #1 tag size is determined as 144 bps INFO @ Tue, 02 Aug 2022 17:18:11: #1 tag size = 144 INFO @ Tue, 02 Aug 2022 17:18:11: #1 total tags in treatment: 11241637 INFO @ Tue, 02 Aug 2022 17:18:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:18:11: #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 17:18:11: 18000000 INFO @ Tue, 02 Aug 2022 17:18:11: #1 tags after filtering in treatment: 9967407 INFO @ Tue, 02 Aug 2022 17:18:11: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 02 Aug 2022 17:18:11: #1 finished! INFO @ Tue, 02 Aug 2022 17:18:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:18:12: #2 number of paired peaks: 2055 INFO @ Tue, 02 Aug 2022 17:18:12: start model_add_line... INFO @ Tue, 02 Aug 2022 17:18:12: start X-correlation... INFO @ Tue, 02 Aug 2022 17:18:12: #2 number of paired peaks: 2055 INFO @ Tue, 02 Aug 2022 17:18:12: start model_add_line... INFO @ Tue, 02 Aug 2022 17:18:12: start X-correlation... INFO @ Tue, 02 Aug 2022 17:18:12: end of X-cor INFO @ Tue, 02 Aug 2022 17:18:12: #2 finished! INFO @ Tue, 02 Aug 2022 17:18:12: #2 predicted fragment length is 258 bps INFO @ Tue, 02 Aug 2022 17:18:12: #2 alternative fragment length(s) may be 258 bps INFO @ Tue, 02 Aug 2022 17:18:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.10_model.r INFO @ Tue, 02 Aug 2022 17:18:12: end of X-cor INFO @ Tue, 02 Aug 2022 17:18:12: #2 finished! INFO @ Tue, 02 Aug 2022 17:18:12: #2 predicted fragment length is 258 bps INFO @ Tue, 02 Aug 2022 17:18:12: #2 alternative fragment length(s) may be 258 bps INFO @ Tue, 02 Aug 2022 17:18:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.05_model.r WARNING @ Tue, 02 Aug 2022 17:18:12: #2 Since the d (258) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:18:12: #2 You may need to consider one of the other alternative d(s): 258 WARNING @ Tue, 02 Aug 2022 17:18:12: #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 17:18:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:18:12: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 02 Aug 2022 17:18:12: #2 Since the d (258) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:18:12: #2 You may need to consider one of the other alternative d(s): 258 WARNING @ Tue, 02 Aug 2022 17:18:12: #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 17:18:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:18:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:18:25: 19000000 INFO @ Tue, 02 Aug 2022 17:18:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:18:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:18:38: 20000000 INFO @ Tue, 02 Aug 2022 17:18:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:18:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:18:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.05_summits.bed INFO @ Tue, 02 Aug 2022 17:18:49: Done! INFO @ Tue, 02 Aug 2022 17:18:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:18:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:18:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.10_summits.bed INFO @ Tue, 02 Aug 2022 17:18:50: Done! pass1 - making usageList (15 chroms): 19 millis pass2 - checking and writing primary data (7076 records, 4 fields): 72 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5208 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:18:52: 21000000 INFO @ Tue, 02 Aug 2022 17:19:06: 22000000 INFO @ Tue, 02 Aug 2022 17:19:20: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:19:33: 24000000 INFO @ Tue, 02 Aug 2022 17:19:45: #1 tag size is determined as 144 bps INFO @ Tue, 02 Aug 2022 17:19:45: #1 tag size = 144 INFO @ Tue, 02 Aug 2022 17:19:45: #1 total tags in treatment: 11241637 INFO @ Tue, 02 Aug 2022 17:19:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:19:45: #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 17:19:45: #1 tags after filtering in treatment: 9967407 INFO @ Tue, 02 Aug 2022 17:19:45: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 02 Aug 2022 17:19:45: #1 finished! INFO @ Tue, 02 Aug 2022 17:19:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:19:46: #2 number of paired peaks: 2055 INFO @ Tue, 02 Aug 2022 17:19:46: start model_add_line... INFO @ Tue, 02 Aug 2022 17:19:46: start X-correlation... INFO @ Tue, 02 Aug 2022 17:19:46: end of X-cor INFO @ Tue, 02 Aug 2022 17:19:46: #2 finished! INFO @ Tue, 02 Aug 2022 17:19:46: #2 predicted fragment length is 258 bps INFO @ Tue, 02 Aug 2022 17:19:46: #2 alternative fragment length(s) may be 258 bps INFO @ Tue, 02 Aug 2022 17:19:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.20_model.r WARNING @ Tue, 02 Aug 2022 17:19:46: #2 Since the d (258) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:19:46: #2 You may need to consider one of the other alternative d(s): 258 WARNING @ Tue, 02 Aug 2022 17:19:46: #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 17:19:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:19:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:20:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:20:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:20:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:20:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499371/SRX11499371.20_summits.bed INFO @ Tue, 02 Aug 2022 17:20:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3444 records, 4 fields): 76 millis CompletedMACS2peakCalling