Job ID = 14167056 SRX = SRX10412043 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13484348 spots for SRR14035718/SRR14035718.sra Written 13484348 spots for SRR14035718/SRR14035718.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167592 ("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: 00:58:36 13484348 reads; of these: 13484348 (100.00%) were paired; of these: 1948142 (14.45%) aligned concordantly 0 times 7815176 (57.96%) aligned concordantly exactly 1 time 3721030 (27.60%) aligned concordantly >1 times ---- 1948142 pairs aligned concordantly 0 times; of these: 576901 (29.61%) aligned discordantly 1 time ---- 1371241 pairs aligned 0 times concordantly or discordantly; of these: 2742482 mates make up the pairs; of these: 1931380 (70.42%) aligned 0 times 205064 (7.48%) aligned exactly 1 time 606038 (22.10%) aligned >1 times 92.84% overall alignment rate Time searching: 00:58:36 Overall time: 00:58:36 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 20 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] 2653632 / 12032096 = 0.2205 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 @ Fri, 10 Dec 2021 10:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.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 @ Fri, 10 Dec 2021 10:37:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:37:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:37:09: 1000000 INFO @ Fri, 10 Dec 2021 10:37:17: 2000000 INFO @ Fri, 10 Dec 2021 10:37:26: 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 @ Fri, 10 Dec 2021 10:37:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.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 @ Fri, 10 Dec 2021 10:37:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:37:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:37:35: 4000000 INFO @ Fri, 10 Dec 2021 10:37:41: 1000000 INFO @ Fri, 10 Dec 2021 10:37:44: 5000000 INFO @ Fri, 10 Dec 2021 10:37:50: 2000000 INFO @ Fri, 10 Dec 2021 10:37:54: 6000000 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 @ Fri, 10 Dec 2021 10:38:00: 3000000 INFO @ Fri, 10 Dec 2021 10:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.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 @ Fri, 10 Dec 2021 10:38:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:38:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:38:04: 7000000 INFO @ Fri, 10 Dec 2021 10:38:11: 4000000 INFO @ Fri, 10 Dec 2021 10:38:13: 1000000 INFO @ Fri, 10 Dec 2021 10:38:16: 8000000 INFO @ Fri, 10 Dec 2021 10:38:23: 5000000 INFO @ Fri, 10 Dec 2021 10:38:25: 2000000 INFO @ Fri, 10 Dec 2021 10:38:27: 9000000 INFO @ Fri, 10 Dec 2021 10:38:35: 6000000 INFO @ Fri, 10 Dec 2021 10:38:37: 3000000 INFO @ Fri, 10 Dec 2021 10:38:39: 10000000 INFO @ Fri, 10 Dec 2021 10:38:46: 7000000 INFO @ Fri, 10 Dec 2021 10:38:50: 4000000 INFO @ Fri, 10 Dec 2021 10:38:51: 11000000 INFO @ Fri, 10 Dec 2021 10:38:58: 8000000 INFO @ Fri, 10 Dec 2021 10:39:02: 5000000 INFO @ Fri, 10 Dec 2021 10:39:02: 12000000 INFO @ Fri, 10 Dec 2021 10:39:09: 9000000 INFO @ Fri, 10 Dec 2021 10:39:14: 13000000 INFO @ Fri, 10 Dec 2021 10:39:14: 6000000 INFO @ Fri, 10 Dec 2021 10:39:21: 10000000 INFO @ Fri, 10 Dec 2021 10:39:25: 14000000 INFO @ Fri, 10 Dec 2021 10:39:27: 7000000 INFO @ Fri, 10 Dec 2021 10:39:32: 11000000 INFO @ Fri, 10 Dec 2021 10:39:37: 15000000 INFO @ Fri, 10 Dec 2021 10:39:39: 8000000 INFO @ Fri, 10 Dec 2021 10:39:43: 12000000 INFO @ Fri, 10 Dec 2021 10:39:48: 16000000 INFO @ Fri, 10 Dec 2021 10:39:52: 9000000 INFO @ Fri, 10 Dec 2021 10:39:55: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:40:00: 17000000 INFO @ Fri, 10 Dec 2021 10:40:04: 10000000 INFO @ Fri, 10 Dec 2021 10:40:06: 14000000 INFO @ Fri, 10 Dec 2021 10:40:12: 18000000 INFO @ Fri, 10 Dec 2021 10:40:16: 11000000 INFO @ Fri, 10 Dec 2021 10:40:18: 15000000 INFO @ Fri, 10 Dec 2021 10:40:23: 19000000 INFO @ Fri, 10 Dec 2021 10:40:29: 12000000 INFO @ Fri, 10 Dec 2021 10:40:29: 16000000 INFO @ Fri, 10 Dec 2021 10:40:31: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:40:31: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:40:31: #1 total tags in treatment: 8977028 INFO @ Fri, 10 Dec 2021 10:40:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:40:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:40:31: #1 tags after filtering in treatment: 8441679 INFO @ Fri, 10 Dec 2021 10:40:31: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 10:40:31: #1 finished! INFO @ Fri, 10 Dec 2021 10:40:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:40:32: #2 number of paired peaks: 361 WARNING @ Fri, 10 Dec 2021 10:40:32: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 10 Dec 2021 10:40:32: start model_add_line... INFO @ Fri, 10 Dec 2021 10:40:32: start X-correlation... INFO @ Fri, 10 Dec 2021 10:40:32: end of X-cor INFO @ Fri, 10 Dec 2021 10:40:32: #2 finished! INFO @ Fri, 10 Dec 2021 10:40:32: #2 predicted fragment length is 179 bps INFO @ Fri, 10 Dec 2021 10:40:32: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 10 Dec 2021 10:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.05_model.r WARNING @ Fri, 10 Dec 2021 10:40:32: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:40:32: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Fri, 10 Dec 2021 10:40:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 10:40:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:40:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:40:40: 17000000 INFO @ Fri, 10 Dec 2021 10:40:41: 13000000 INFO @ Fri, 10 Dec 2021 10:40:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:40:51: 18000000 INFO @ Fri, 10 Dec 2021 10:40:54: 14000000 INFO @ Fri, 10 Dec 2021 10:40:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:40:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:40:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.05_summits.bed INFO @ Fri, 10 Dec 2021 10:40:59: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (3285 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:41:01: 19000000 INFO @ Fri, 10 Dec 2021 10:41:06: 15000000 INFO @ Fri, 10 Dec 2021 10:41:09: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:41:09: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:41:09: #1 total tags in treatment: 8977028 INFO @ Fri, 10 Dec 2021 10:41:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:41:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:41:09: #1 tags after filtering in treatment: 8441679 INFO @ Fri, 10 Dec 2021 10:41:09: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 10:41:09: #1 finished! INFO @ Fri, 10 Dec 2021 10:41:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:41:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:41:10: #2 number of paired peaks: 361 WARNING @ Fri, 10 Dec 2021 10:41:10: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 10 Dec 2021 10:41:10: start model_add_line... INFO @ Fri, 10 Dec 2021 10:41:10: start X-correlation... INFO @ Fri, 10 Dec 2021 10:41:10: end of X-cor INFO @ Fri, 10 Dec 2021 10:41:10: #2 finished! INFO @ Fri, 10 Dec 2021 10:41:10: #2 predicted fragment length is 179 bps INFO @ Fri, 10 Dec 2021 10:41:10: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 10 Dec 2021 10:41:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.10_model.r WARNING @ Fri, 10 Dec 2021 10:41:10: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:41:10: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Fri, 10 Dec 2021 10:41:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 10:41:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:41:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:41:17: 16000000 INFO @ Fri, 10 Dec 2021 10:41:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:41:28: 17000000 INFO @ Fri, 10 Dec 2021 10:41:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:41:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:41:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.10_summits.bed INFO @ Fri, 10 Dec 2021 10:41:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1378 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:41:40: 18000000 INFO @ Fri, 10 Dec 2021 10:41:51: 19000000 INFO @ Fri, 10 Dec 2021 10:41:58: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:41:58: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:41:58: #1 total tags in treatment: 8977028 INFO @ Fri, 10 Dec 2021 10:41:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:41:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:41:58: #1 tags after filtering in treatment: 8441679 INFO @ Fri, 10 Dec 2021 10:41:58: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 10:41:58: #1 finished! INFO @ Fri, 10 Dec 2021 10:41:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:41:59: #2 number of paired peaks: 361 WARNING @ Fri, 10 Dec 2021 10:41:59: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 10 Dec 2021 10:41:59: start model_add_line... INFO @ Fri, 10 Dec 2021 10:41:59: start X-correlation... INFO @ Fri, 10 Dec 2021 10:41:59: end of X-cor INFO @ Fri, 10 Dec 2021 10:41:59: #2 finished! INFO @ Fri, 10 Dec 2021 10:41:59: #2 predicted fragment length is 179 bps INFO @ Fri, 10 Dec 2021 10:41:59: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 10 Dec 2021 10:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.20_model.r WARNING @ Fri, 10 Dec 2021 10:41:59: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:41:59: #2 You may need to consider one of the other alternative d(s): 179 WARNING @ Fri, 10 Dec 2021 10:41:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 10:41:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:42:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:42:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:42:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:42:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412043/SRX10412043.20_summits.bed INFO @ Fri, 10 Dec 2021 10:42:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (705 records, 4 fields): 2 millis CompletedMACS2peakCalling