Job ID = 12266684 SRX = SRX8622119 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29850858 spots for SRR12096679/SRR12096679.sra Written 29850858 spots for SRR12096679/SRR12096679.sra fastq に変換しました。 bowtie でマッピング中... Your job 12268323 ("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: 01:12:31 29850858 reads; of these: 29850858 (100.00%) were paired; of these: 26792495 (89.75%) aligned concordantly 0 times 2079090 (6.96%) aligned concordantly exactly 1 time 979273 (3.28%) aligned concordantly >1 times ---- 26792495 pairs aligned concordantly 0 times; of these: 1766783 (6.59%) aligned discordantly 1 time ---- 25025712 pairs aligned 0 times concordantly or discordantly; of these: 50051424 mates make up the pairs; of these: 48296429 (96.49%) aligned 0 times 397265 (0.79%) aligned exactly 1 time 1357730 (2.71%) aligned >1 times 19.10% overall alignment rate Time searching: 01:12:31 Overall time: 01:12:31 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 12 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] 581243 / 4750405 = 0.1224 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 10:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.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 @ Sat, 03 Apr 2021 10:39:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:39:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:39:39: 1000000 INFO @ Sat, 03 Apr 2021 10:39:47: 2000000 INFO @ Sat, 03 Apr 2021 10:39:55: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 10:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.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 @ Sat, 03 Apr 2021 10:39:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:39:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:40:04: 4000000 INFO @ Sat, 03 Apr 2021 10:40:09: 1000000 INFO @ Sat, 03 Apr 2021 10:40:13: 5000000 INFO @ Sat, 03 Apr 2021 10:40:18: 2000000 INFO @ Sat, 03 Apr 2021 10:40:22: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 10:40:27: 3000000 INFO @ Sat, 03 Apr 2021 10:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.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 @ Sat, 03 Apr 2021 10:40:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:40:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:40:32: 7000000 INFO @ Sat, 03 Apr 2021 10:40:37: 4000000 INFO @ Sat, 03 Apr 2021 10:40:40: 1000000 INFO @ Sat, 03 Apr 2021 10:40:42: 8000000 INFO @ Sat, 03 Apr 2021 10:40:47: 5000000 INFO @ Sat, 03 Apr 2021 10:40:50: 2000000 INFO @ Sat, 03 Apr 2021 10:40:52: 9000000 INFO @ Sat, 03 Apr 2021 10:40:56: 6000000 INFO @ Sat, 03 Apr 2021 10:41:00: 3000000 INFO @ Sat, 03 Apr 2021 10:41:01: 10000000 INFO @ Sat, 03 Apr 2021 10:41:04: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 10:41:04: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 10:41:04: #1 total tags in treatment: 2661403 INFO @ Sat, 03 Apr 2021 10:41:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:41:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 10:41:04: #1 tags after filtering in treatment: 2340495 INFO @ Sat, 03 Apr 2021 10:41:04: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 03 Apr 2021 10:41:04: #1 finished! INFO @ Sat, 03 Apr 2021 10:41:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:41:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:41:04: #2 number of paired peaks: 2328 INFO @ Sat, 03 Apr 2021 10:41:04: start model_add_line... INFO @ Sat, 03 Apr 2021 10:41:04: start X-correlation... INFO @ Sat, 03 Apr 2021 10:41:04: end of X-cor INFO @ Sat, 03 Apr 2021 10:41:04: #2 finished! INFO @ Sat, 03 Apr 2021 10:41:04: #2 predicted fragment length is 184 bps INFO @ Sat, 03 Apr 2021 10:41:04: #2 alternative fragment length(s) may be 184 bps INFO @ Sat, 03 Apr 2021 10:41:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.05_model.r WARNING @ Sat, 03 Apr 2021 10:41:04: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:41:04: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Sat, 03 Apr 2021 10:41:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:41:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:41:06: 7000000 INFO @ Sat, 03 Apr 2021 10:41:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:41:09: 4000000 INFO @ Sat, 03 Apr 2021 10:41:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.05_peaks.xls INFO @ Sat, 03 Apr 2021 10:41:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:41:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.05_summits.bed INFO @ Sat, 03 Apr 2021 10:41:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6381 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:41:15: 8000000 INFO @ Sat, 03 Apr 2021 10:41:18: 5000000 INFO @ Sat, 03 Apr 2021 10:41:24: 9000000 INFO @ Sat, 03 Apr 2021 10:41:27: 6000000 INFO @ Sat, 03 Apr 2021 10:41:33: 10000000 INFO @ Sat, 03 Apr 2021 10:41:36: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 10:41:36: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 10:41:36: #1 total tags in treatment: 2661403 INFO @ Sat, 03 Apr 2021 10:41:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:41:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 10:41:36: #1 tags after filtering in treatment: 2340495 INFO @ Sat, 03 Apr 2021 10:41:36: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 03 Apr 2021 10:41:36: #1 finished! INFO @ Sat, 03 Apr 2021 10:41:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:41:36: #2 number of paired peaks: 2328 INFO @ Sat, 03 Apr 2021 10:41:36: start model_add_line... INFO @ Sat, 03 Apr 2021 10:41:36: start X-correlation... INFO @ Sat, 03 Apr 2021 10:41:36: end of X-cor INFO @ Sat, 03 Apr 2021 10:41:36: #2 finished! INFO @ Sat, 03 Apr 2021 10:41:36: #2 predicted fragment length is 184 bps INFO @ Sat, 03 Apr 2021 10:41:36: #2 alternative fragment length(s) may be 184 bps INFO @ Sat, 03 Apr 2021 10:41:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.10_model.r WARNING @ Sat, 03 Apr 2021 10:41:36: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:41:36: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Sat, 03 Apr 2021 10:41:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:41:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:41:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:41:36: 7000000 INFO @ Sat, 03 Apr 2021 10:41:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.10_peaks.xls INFO @ Sat, 03 Apr 2021 10:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.10_summits.bed INFO @ Sat, 03 Apr 2021 10:41:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1773 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:41:44: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 10:41:53: 9000000 INFO @ Sat, 03 Apr 2021 10:42:01: 10000000 INFO @ Sat, 03 Apr 2021 10:42:02: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 10:42:02: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 10:42:02: #1 total tags in treatment: 2661403 INFO @ Sat, 03 Apr 2021 10:42:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:42:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 10:42:03: #1 tags after filtering in treatment: 2340495 INFO @ Sat, 03 Apr 2021 10:42:03: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 03 Apr 2021 10:42:03: #1 finished! INFO @ Sat, 03 Apr 2021 10:42:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:42:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:42:03: #2 number of paired peaks: 2328 INFO @ Sat, 03 Apr 2021 10:42:03: start model_add_line... INFO @ Sat, 03 Apr 2021 10:42:03: start X-correlation... INFO @ Sat, 03 Apr 2021 10:42:03: end of X-cor INFO @ Sat, 03 Apr 2021 10:42:03: #2 finished! INFO @ Sat, 03 Apr 2021 10:42:03: #2 predicted fragment length is 184 bps INFO @ Sat, 03 Apr 2021 10:42:03: #2 alternative fragment length(s) may be 184 bps INFO @ Sat, 03 Apr 2021 10:42:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.20_model.r WARNING @ Sat, 03 Apr 2021 10:42:03: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:42:03: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Sat, 03 Apr 2021 10:42:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:42:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:42:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:42:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:42:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.20_peaks.xls INFO @ Sat, 03 Apr 2021 10:42:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:42:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622119/SRX8622119.20_summits.bed INFO @ Sat, 03 Apr 2021 10:42:10: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。