Job ID = 14171974 SRX = SRX7889134 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26068945 spots for SRR11283124/SRR11283124.sra Written 26068945 spots for SRR11283124/SRR11283124.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172636 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:02:07 26068945 reads; of these: 26068945 (100.00%) were paired; of these: 8546111 (32.78%) aligned concordantly 0 times 13961447 (53.56%) aligned concordantly exactly 1 time 3561387 (13.66%) aligned concordantly >1 times ---- 8546111 pairs aligned concordantly 0 times; of these: 1576857 (18.45%) aligned discordantly 1 time ---- 6969254 pairs aligned 0 times concordantly or discordantly; of these: 13938508 mates make up the pairs; of these: 11275340 (80.89%) aligned 0 times 1595200 (11.44%) aligned exactly 1 time 1067968 (7.66%) aligned >1 times 78.37% overall alignment rate Time searching: 01:02:08 Overall time: 01:02:08 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] 5118264 / 17541996 = 0.2918 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.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, 11 Dec 2021 15:03:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:03:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:03:13: 1000000 INFO @ Sat, 11 Dec 2021 15:03:20: 2000000 INFO @ Sat, 11 Dec 2021 15:03:27: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:03:34: 4000000 INFO @ Sat, 11 Dec 2021 15:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.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, 11 Dec 2021 15:03:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:03:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:03:42: 5000000 INFO @ Sat, 11 Dec 2021 15:03:45: 1000000 INFO @ Sat, 11 Dec 2021 15:03:50: 6000000 INFO @ Sat, 11 Dec 2021 15:03:54: 2000000 INFO @ Sat, 11 Dec 2021 15:03:58: 7000000 INFO @ Sat, 11 Dec 2021 15:04:04: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.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, 11 Dec 2021 15:04:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:04:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:04:06: 8000000 INFO @ Sat, 11 Dec 2021 15:04:13: 4000000 INFO @ Sat, 11 Dec 2021 15:04:14: 9000000 INFO @ Sat, 11 Dec 2021 15:04:15: 1000000 INFO @ Sat, 11 Dec 2021 15:04:22: 10000000 INFO @ Sat, 11 Dec 2021 15:04:23: 5000000 INFO @ Sat, 11 Dec 2021 15:04:25: 2000000 INFO @ Sat, 11 Dec 2021 15:04:31: 11000000 INFO @ Sat, 11 Dec 2021 15:04:32: 6000000 INFO @ Sat, 11 Dec 2021 15:04:35: 3000000 INFO @ Sat, 11 Dec 2021 15:04:40: 12000000 INFO @ Sat, 11 Dec 2021 15:04:42: 7000000 INFO @ Sat, 11 Dec 2021 15:04:45: 4000000 INFO @ Sat, 11 Dec 2021 15:04:48: 13000000 INFO @ Sat, 11 Dec 2021 15:04:52: 8000000 INFO @ Sat, 11 Dec 2021 15:04:55: 5000000 INFO @ Sat, 11 Dec 2021 15:04:57: 14000000 INFO @ Sat, 11 Dec 2021 15:05:02: 9000000 INFO @ Sat, 11 Dec 2021 15:05:05: 6000000 INFO @ Sat, 11 Dec 2021 15:05:05: 15000000 INFO @ Sat, 11 Dec 2021 15:05:12: 10000000 INFO @ Sat, 11 Dec 2021 15:05:13: 16000000 INFO @ Sat, 11 Dec 2021 15:05:15: 7000000 INFO @ Sat, 11 Dec 2021 15:05:22: 11000000 INFO @ Sat, 11 Dec 2021 15:05:22: 17000000 INFO @ Sat, 11 Dec 2021 15:05:25: 8000000 INFO @ Sat, 11 Dec 2021 15:05:30: 18000000 INFO @ Sat, 11 Dec 2021 15:05:32: 12000000 INFO @ Sat, 11 Dec 2021 15:05:35: 9000000 INFO @ Sat, 11 Dec 2021 15:05:39: 19000000 INFO @ Sat, 11 Dec 2021 15:05:42: 13000000 INFO @ Sat, 11 Dec 2021 15:05:44: 10000000 INFO @ Sat, 11 Dec 2021 15:05:47: 20000000 INFO @ Sat, 11 Dec 2021 15:05:51: 14000000 INFO @ Sat, 11 Dec 2021 15:05:54: 11000000 INFO @ Sat, 11 Dec 2021 15:05:55: 21000000 INFO @ Sat, 11 Dec 2021 15:06:01: 15000000 INFO @ Sat, 11 Dec 2021 15:06:03: 22000000 INFO @ Sat, 11 Dec 2021 15:06:04: 12000000 INFO @ Sat, 11 Dec 2021 15:06:11: 16000000 INFO @ Sat, 11 Dec 2021 15:06:11: 23000000 INFO @ Sat, 11 Dec 2021 15:06:13: 13000000 INFO @ Sat, 11 Dec 2021 15:06:20: 24000000 INFO @ Sat, 11 Dec 2021 15:06:21: 17000000 INFO @ Sat, 11 Dec 2021 15:06:23: 14000000 INFO @ Sat, 11 Dec 2021 15:06:28: 25000000 INFO @ Sat, 11 Dec 2021 15:06:30: 18000000 INFO @ Sat, 11 Dec 2021 15:06:31: 15000000 INFO @ Sat, 11 Dec 2021 15:06:37: 26000000 INFO @ Sat, 11 Dec 2021 15:06:40: 16000000 INFO @ Sat, 11 Dec 2021 15:06:40: 19000000 INFO @ Sat, 11 Dec 2021 15:06:45: 27000000 INFO @ Sat, 11 Dec 2021 15:06:49: 17000000 INFO @ Sat, 11 Dec 2021 15:06:50: 20000000 INFO @ Sat, 11 Dec 2021 15:06:54: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:06:58: 18000000 INFO @ Sat, 11 Dec 2021 15:06:59: 21000000 INFO @ Sat, 11 Dec 2021 15:07:02: 29000000 INFO @ Sat, 11 Dec 2021 15:07:07: 19000000 INFO @ Sat, 11 Dec 2021 15:07:09: 22000000 INFO @ Sat, 11 Dec 2021 15:07:11: 30000000 INFO @ Sat, 11 Dec 2021 15:07:15: 20000000 INFO @ Sat, 11 Dec 2021 15:07:16: #1 tag size is determined as 134 bps INFO @ Sat, 11 Dec 2021 15:07:16: #1 tag size = 134 INFO @ Sat, 11 Dec 2021 15:07:16: #1 total tags in treatment: 12748361 INFO @ Sat, 11 Dec 2021 15:07:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:07:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:07:16: #1 tags after filtering in treatment: 10844290 INFO @ Sat, 11 Dec 2021 15:07:16: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 15:07:16: #1 finished! INFO @ Sat, 11 Dec 2021 15:07:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:07:17: #2 number of paired peaks: 1386 INFO @ Sat, 11 Dec 2021 15:07:17: start model_add_line... INFO @ Sat, 11 Dec 2021 15:07:17: start X-correlation... INFO @ Sat, 11 Dec 2021 15:07:17: end of X-cor INFO @ Sat, 11 Dec 2021 15:07:17: #2 finished! INFO @ Sat, 11 Dec 2021 15:07:17: #2 predicted fragment length is 252 bps INFO @ Sat, 11 Dec 2021 15:07:17: #2 alternative fragment length(s) may be 252 bps INFO @ Sat, 11 Dec 2021 15:07:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.05_model.r WARNING @ Sat, 11 Dec 2021 15:07:17: #2 Since the d (252) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:07:17: #2 You may need to consider one of the other alternative d(s): 252 WARNING @ Sat, 11 Dec 2021 15:07:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:07:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:07:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:07:18: 23000000 INFO @ Sat, 11 Dec 2021 15:07:23: 21000000 INFO @ Sat, 11 Dec 2021 15:07:28: 24000000 INFO @ Sat, 11 Dec 2021 15:07:31: 22000000 INFO @ Sat, 11 Dec 2021 15:07:37: 25000000 INFO @ Sat, 11 Dec 2021 15:07:40: 23000000 INFO @ Sat, 11 Dec 2021 15:07:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:07:47: 26000000 INFO @ Sat, 11 Dec 2021 15:07:48: 24000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.05_summits.bed INFO @ Sat, 11 Dec 2021 15:07:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7272 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:07:56: 25000000 INFO @ Sat, 11 Dec 2021 15:07:56: 27000000 INFO @ Sat, 11 Dec 2021 15:08:04: 26000000 INFO @ Sat, 11 Dec 2021 15:08:05: 28000000 INFO @ Sat, 11 Dec 2021 15:08:13: 27000000 INFO @ Sat, 11 Dec 2021 15:08:15: 29000000 INFO @ Sat, 11 Dec 2021 15:08:21: 28000000 INFO @ Sat, 11 Dec 2021 15:08:24: 30000000 INFO @ Sat, 11 Dec 2021 15:08:29: 29000000 INFO @ Sat, 11 Dec 2021 15:08:30: #1 tag size is determined as 134 bps INFO @ Sat, 11 Dec 2021 15:08:30: #1 tag size = 134 INFO @ Sat, 11 Dec 2021 15:08:30: #1 total tags in treatment: 12748361 INFO @ Sat, 11 Dec 2021 15:08:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:08:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:08:30: #1 tags after filtering in treatment: 10844290 INFO @ Sat, 11 Dec 2021 15:08:30: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 15:08:30: #1 finished! INFO @ Sat, 11 Dec 2021 15:08:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:08:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:08:31: #2 number of paired peaks: 1386 INFO @ Sat, 11 Dec 2021 15:08:31: start model_add_line... INFO @ Sat, 11 Dec 2021 15:08:31: start X-correlation... INFO @ Sat, 11 Dec 2021 15:08:31: end of X-cor INFO @ Sat, 11 Dec 2021 15:08:31: #2 finished! INFO @ Sat, 11 Dec 2021 15:08:31: #2 predicted fragment length is 252 bps INFO @ Sat, 11 Dec 2021 15:08:31: #2 alternative fragment length(s) may be 252 bps INFO @ Sat, 11 Dec 2021 15:08:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.10_model.r WARNING @ Sat, 11 Dec 2021 15:08:31: #2 Since the d (252) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:08:31: #2 You may need to consider one of the other alternative d(s): 252 WARNING @ Sat, 11 Dec 2021 15:08:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:08:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:08:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:08:37: 30000000 INFO @ Sat, 11 Dec 2021 15:08:42: #1 tag size is determined as 134 bps INFO @ Sat, 11 Dec 2021 15:08:42: #1 tag size = 134 INFO @ Sat, 11 Dec 2021 15:08:42: #1 total tags in treatment: 12748361 INFO @ Sat, 11 Dec 2021 15:08:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:08:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:08:42: #1 tags after filtering in treatment: 10844290 INFO @ Sat, 11 Dec 2021 15:08:42: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 15:08:42: #1 finished! INFO @ Sat, 11 Dec 2021 15:08:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:08:43: #2 number of paired peaks: 1386 INFO @ Sat, 11 Dec 2021 15:08:43: start model_add_line... INFO @ Sat, 11 Dec 2021 15:08:43: start X-correlation... INFO @ Sat, 11 Dec 2021 15:08:43: end of X-cor INFO @ Sat, 11 Dec 2021 15:08:43: #2 finished! INFO @ Sat, 11 Dec 2021 15:08:43: #2 predicted fragment length is 252 bps INFO @ Sat, 11 Dec 2021 15:08:43: #2 alternative fragment length(s) may be 252 bps INFO @ Sat, 11 Dec 2021 15:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.20_model.r WARNING @ Sat, 11 Dec 2021 15:08:43: #2 Since the d (252) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:08:43: #2 You may need to consider one of the other alternative d(s): 252 WARNING @ Sat, 11 Dec 2021 15:08:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:08:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:08:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:09:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:09:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:09:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.10_summits.bed INFO @ Sat, 11 Dec 2021 15:09:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4643 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:09:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:09:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:09:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:09:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889134/SRX7889134.20_summits.bed INFO @ Sat, 11 Dec 2021 15:09:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2676 records, 4 fields): 4 millis CompletedMACS2peakCalling