Job ID = 16439389 SRX = SRX13453890 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8719750 spots for SRR17276248/SRR17276248.sra Written 8719750 spots for SRR17276248/SRR17276248.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439589 ("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: 00:29:15 8719750 reads; of these: 8719750 (100.00%) were paired; of these: 1187144 (13.61%) aligned concordantly 0 times 5586067 (64.06%) aligned concordantly exactly 1 time 1946539 (22.32%) aligned concordantly >1 times ---- 1187144 pairs aligned concordantly 0 times; of these: 593519 (50.00%) aligned discordantly 1 time ---- 593625 pairs aligned 0 times concordantly or discordantly; of these: 1187250 mates make up the pairs; of these: 601589 (50.67%) aligned 0 times 219361 (18.48%) aligned exactly 1 time 366300 (30.85%) aligned >1 times 96.55% overall alignment rate Time searching: 00:29:15 Overall time: 00:29:15 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 8 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] 139317 / 7961696 = 0.0175 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 15:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.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 15:41:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:41:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:41:26: 1000000 INFO @ Tue, 02 Aug 2022 15:41:38: 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 15:41:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.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 15:41:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:41:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:41:50: 3000000 INFO @ Tue, 02 Aug 2022 15:41:58: 1000000 INFO @ Tue, 02 Aug 2022 15:42:03: 4000000 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 15:42:12: 2000000 INFO @ Tue, 02 Aug 2022 15:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.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 15:42:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:42:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:42:16: 5000000 INFO @ Tue, 02 Aug 2022 15:42:25: 1000000 INFO @ Tue, 02 Aug 2022 15:42:26: 3000000 INFO @ Tue, 02 Aug 2022 15:42:29: 6000000 INFO @ Tue, 02 Aug 2022 15:42:35: 2000000 INFO @ Tue, 02 Aug 2022 15:42:41: 4000000 INFO @ Tue, 02 Aug 2022 15:42:42: 7000000 INFO @ Tue, 02 Aug 2022 15:42:46: 3000000 INFO @ Tue, 02 Aug 2022 15:42:55: 8000000 INFO @ Tue, 02 Aug 2022 15:42:55: 5000000 INFO @ Tue, 02 Aug 2022 15:42:57: 4000000 INFO @ Tue, 02 Aug 2022 15:43:08: 9000000 INFO @ Tue, 02 Aug 2022 15:43:09: 5000000 INFO @ Tue, 02 Aug 2022 15:43:10: 6000000 INFO @ Tue, 02 Aug 2022 15:43:21: 6000000 INFO @ Tue, 02 Aug 2022 15:43:22: 10000000 INFO @ Tue, 02 Aug 2022 15:43:24: 7000000 INFO @ Tue, 02 Aug 2022 15:43:33: 7000000 INFO @ Tue, 02 Aug 2022 15:43:35: 11000000 INFO @ Tue, 02 Aug 2022 15:43:38: 8000000 INFO @ Tue, 02 Aug 2022 15:43:44: 8000000 INFO @ Tue, 02 Aug 2022 15:43:48: 12000000 INFO @ Tue, 02 Aug 2022 15:43:53: 9000000 INFO @ Tue, 02 Aug 2022 15:43:56: 9000000 INFO @ Tue, 02 Aug 2022 15:44:01: 13000000 INFO @ Tue, 02 Aug 2022 15:44:07: 10000000 INFO @ Tue, 02 Aug 2022 15:44:07: 10000000 INFO @ Tue, 02 Aug 2022 15:44:14: 14000000 INFO @ Tue, 02 Aug 2022 15:44:20: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:44:22: 11000000 INFO @ Tue, 02 Aug 2022 15:44:28: 15000000 INFO @ Tue, 02 Aug 2022 15:44:31: 12000000 INFO @ Tue, 02 Aug 2022 15:44:37: 12000000 INFO @ Tue, 02 Aug 2022 15:44:42: 16000000 INFO @ Tue, 02 Aug 2022 15:44:42: 13000000 INFO @ Tue, 02 Aug 2022 15:44:49: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:44:49: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:44:49: #1 total tags in treatment: 7394058 INFO @ Tue, 02 Aug 2022 15:44:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:44:49: #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 15:44:50: #1 tags after filtering in treatment: 7168396 INFO @ Tue, 02 Aug 2022 15:44:50: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:44:50: #1 finished! INFO @ Tue, 02 Aug 2022 15:44:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:44:50: #2 number of paired peaks: 136 WARNING @ Tue, 02 Aug 2022 15:44:50: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Tue, 02 Aug 2022 15:44:50: start model_add_line... INFO @ Tue, 02 Aug 2022 15:44:50: start X-correlation... INFO @ Tue, 02 Aug 2022 15:44:51: end of X-cor INFO @ Tue, 02 Aug 2022 15:44:51: #2 finished! INFO @ Tue, 02 Aug 2022 15:44:51: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 15:44:51: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 15:44:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.05_model.r WARNING @ Tue, 02 Aug 2022 15:44:51: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:44:51: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 15:44:51: #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 15:44:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:44:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:44:52: 13000000 INFO @ Tue, 02 Aug 2022 15:44:53: 14000000 INFO @ Tue, 02 Aug 2022 15:45:03: 15000000 INFO @ Tue, 02 Aug 2022 15:45:07: 14000000 INFO @ Tue, 02 Aug 2022 15:45:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:45:14: 16000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:45:20: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:45:20: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:45:20: #1 total tags in treatment: 7394058 INFO @ Tue, 02 Aug 2022 15:45:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:45:20: #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 15:45:20: #1 tags after filtering in treatment: 7168396 INFO @ Tue, 02 Aug 2022 15:45:20: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:45:20: #1 finished! INFO @ Tue, 02 Aug 2022 15:45:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:45:21: #2 number of paired peaks: 136 WARNING @ Tue, 02 Aug 2022 15:45:21: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Tue, 02 Aug 2022 15:45:21: start model_add_line... INFO @ Tue, 02 Aug 2022 15:45:21: start X-correlation... INFO @ Tue, 02 Aug 2022 15:45:21: end of X-cor INFO @ Tue, 02 Aug 2022 15:45:21: #2 finished! INFO @ Tue, 02 Aug 2022 15:45:21: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 15:45:21: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 15:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.20_model.r WARNING @ Tue, 02 Aug 2022 15:45:21: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:45:21: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 15:45:21: #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 15:45:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:45:21: 15000000 INFO @ Tue, 02 Aug 2022 15:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.05_summits.bed INFO @ Tue, 02 Aug 2022 15:45:23: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (793 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:45:36: 16000000 INFO @ Tue, 02 Aug 2022 15:45:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:45:44: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:45:44: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:45:44: #1 total tags in treatment: 7394058 INFO @ Tue, 02 Aug 2022 15:45:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:45:44: #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 15:45:44: #1 tags after filtering in treatment: 7168396 INFO @ Tue, 02 Aug 2022 15:45:44: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:45:44: #1 finished! INFO @ Tue, 02 Aug 2022 15:45:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:45:45: #2 number of paired peaks: 136 WARNING @ Tue, 02 Aug 2022 15:45:45: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Tue, 02 Aug 2022 15:45:45: start model_add_line... INFO @ Tue, 02 Aug 2022 15:45:45: start X-correlation... INFO @ Tue, 02 Aug 2022 15:45:45: end of X-cor INFO @ Tue, 02 Aug 2022 15:45:45: #2 finished! INFO @ Tue, 02 Aug 2022 15:45:45: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 15:45:45: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 15:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.10_model.r WARNING @ Tue, 02 Aug 2022 15:45:45: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:45:45: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 15:45:45: #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 15:45:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.20_summits.bed INFO @ Tue, 02 Aug 2022 15:45:56: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (321 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:46:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:46:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:46:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:46:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453890/SRX13453890.10_summits.bed INFO @ Tue, 02 Aug 2022 15:46:18: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (521 records, 4 fields): 6 millis CompletedMACS2peakCalling