Job ID = 6626993 SRX = SRX7975016 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27576003 spots for SRR11396263/SRR11396263.sra Written 27576003 spots for SRR11396263/SRR11396263.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627338 ("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: 00:57:37 27576003 reads; of these: 27576003 (100.00%) were paired; of these: 10260553 (37.21%) aligned concordantly 0 times 13217583 (47.93%) aligned concordantly exactly 1 time 4097867 (14.86%) aligned concordantly >1 times ---- 10260553 pairs aligned concordantly 0 times; of these: 1384652 (13.49%) aligned discordantly 1 time ---- 8875901 pairs aligned 0 times concordantly or discordantly; of these: 17751802 mates make up the pairs; of these: 15276811 (86.06%) aligned 0 times 1209225 (6.81%) aligned exactly 1 time 1265766 (7.13%) aligned >1 times 72.30% overall alignment rate Time searching: 00:57:37 Overall time: 00:57:37 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] 9251330 / 18675616 = 0.4954 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.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, 14 Jul 2020 10:24:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:24:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:24:06: 1000000 INFO @ Tue, 14 Jul 2020 10:24:11: 2000000 INFO @ Tue, 14 Jul 2020 10:24:17: 3000000 INFO @ Tue, 14 Jul 2020 10:24:22: 4000000 INFO @ Tue, 14 Jul 2020 10:24:28: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.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, 14 Jul 2020 10:24:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:24:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:24:34: 6000000 INFO @ Tue, 14 Jul 2020 10:24:36: 1000000 INFO @ Tue, 14 Jul 2020 10:24:39: 7000000 INFO @ Tue, 14 Jul 2020 10:24:43: 2000000 INFO @ Tue, 14 Jul 2020 10:24:45: 8000000 INFO @ Tue, 14 Jul 2020 10:24:49: 3000000 INFO @ Tue, 14 Jul 2020 10:24:51: 9000000 INFO @ Tue, 14 Jul 2020 10:24:55: 4000000 INFO @ Tue, 14 Jul 2020 10:24:57: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:25:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.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, 14 Jul 2020 10:25:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:25:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:25:02: 5000000 INFO @ Tue, 14 Jul 2020 10:25:03: 11000000 INFO @ Tue, 14 Jul 2020 10:25:07: 1000000 INFO @ Tue, 14 Jul 2020 10:25:08: 6000000 INFO @ Tue, 14 Jul 2020 10:25:08: 12000000 INFO @ Tue, 14 Jul 2020 10:25:13: 2000000 INFO @ Tue, 14 Jul 2020 10:25:14: 13000000 INFO @ Tue, 14 Jul 2020 10:25:14: 7000000 INFO @ Tue, 14 Jul 2020 10:25:19: 14000000 INFO @ Tue, 14 Jul 2020 10:25:20: 8000000 INFO @ Tue, 14 Jul 2020 10:25:20: 3000000 INFO @ Tue, 14 Jul 2020 10:25:25: 15000000 INFO @ Tue, 14 Jul 2020 10:25:26: 9000000 INFO @ Tue, 14 Jul 2020 10:25:27: 4000000 INFO @ Tue, 14 Jul 2020 10:25:31: 16000000 INFO @ Tue, 14 Jul 2020 10:25:32: 10000000 INFO @ Tue, 14 Jul 2020 10:25:34: 5000000 INFO @ Tue, 14 Jul 2020 10:25:37: 17000000 INFO @ Tue, 14 Jul 2020 10:25:37: 11000000 INFO @ Tue, 14 Jul 2020 10:25:41: 6000000 INFO @ Tue, 14 Jul 2020 10:25:43: 12000000 INFO @ Tue, 14 Jul 2020 10:25:43: 18000000 INFO @ Tue, 14 Jul 2020 10:25:48: 7000000 INFO @ Tue, 14 Jul 2020 10:25:49: 13000000 INFO @ Tue, 14 Jul 2020 10:25:49: 19000000 INFO @ Tue, 14 Jul 2020 10:25:54: 14000000 INFO @ Tue, 14 Jul 2020 10:25:55: 8000000 INFO @ Tue, 14 Jul 2020 10:25:55: 20000000 INFO @ Tue, 14 Jul 2020 10:26:00: 15000000 INFO @ Tue, 14 Jul 2020 10:26:01: 21000000 INFO @ Tue, 14 Jul 2020 10:26:02: 9000000 INFO @ Tue, 14 Jul 2020 10:26:03: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 10:26:03: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 10:26:03: #1 total tags in treatment: 8639564 INFO @ Tue, 14 Jul 2020 10:26:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:26:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:26:03: #1 tags after filtering in treatment: 8219308 INFO @ Tue, 14 Jul 2020 10:26:03: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 10:26:03: #1 finished! INFO @ Tue, 14 Jul 2020 10:26:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:26:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:26:04: #2 number of paired peaks: 247 WARNING @ Tue, 14 Jul 2020 10:26:04: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 14 Jul 2020 10:26:04: start model_add_line... INFO @ Tue, 14 Jul 2020 10:26:04: start X-correlation... INFO @ Tue, 14 Jul 2020 10:26:04: end of X-cor INFO @ Tue, 14 Jul 2020 10:26:04: #2 finished! INFO @ Tue, 14 Jul 2020 10:26:04: #2 predicted fragment length is 159 bps INFO @ Tue, 14 Jul 2020 10:26:04: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 14 Jul 2020 10:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.05_model.r WARNING @ Tue, 14 Jul 2020 10:26:04: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:26:04: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Tue, 14 Jul 2020 10:26:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:26:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:26:06: 16000000 INFO @ Tue, 14 Jul 2020 10:26:09: 10000000 INFO @ Tue, 14 Jul 2020 10:26:11: 17000000 INFO @ Tue, 14 Jul 2020 10:26:15: 11000000 INFO @ Tue, 14 Jul 2020 10:26:17: 18000000 INFO @ Tue, 14 Jul 2020 10:26:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:26:22: 12000000 INFO @ Tue, 14 Jul 2020 10:26:23: 19000000 INFO @ Tue, 14 Jul 2020 10:26:28: 13000000 INFO @ Tue, 14 Jul 2020 10:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:26:29: 20000000 INFO @ Tue, 14 Jul 2020 10:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.05_summits.bed INFO @ Tue, 14 Jul 2020 10:26:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3703 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:26:35: 21000000 INFO @ Tue, 14 Jul 2020 10:26:35: 14000000 INFO @ Tue, 14 Jul 2020 10:26:37: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 10:26:37: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 10:26:37: #1 total tags in treatment: 8639564 INFO @ Tue, 14 Jul 2020 10:26:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:26:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:26:37: #1 tags after filtering in treatment: 8219308 INFO @ Tue, 14 Jul 2020 10:26:37: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 10:26:37: #1 finished! INFO @ Tue, 14 Jul 2020 10:26:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:26:38: #2 number of paired peaks: 247 WARNING @ Tue, 14 Jul 2020 10:26:38: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 14 Jul 2020 10:26:38: start model_add_line... INFO @ Tue, 14 Jul 2020 10:26:38: start X-correlation... INFO @ Tue, 14 Jul 2020 10:26:38: end of X-cor INFO @ Tue, 14 Jul 2020 10:26:38: #2 finished! INFO @ Tue, 14 Jul 2020 10:26:38: #2 predicted fragment length is 159 bps INFO @ Tue, 14 Jul 2020 10:26:38: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 14 Jul 2020 10:26:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.10_model.r WARNING @ Tue, 14 Jul 2020 10:26:38: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:26:38: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Tue, 14 Jul 2020 10:26:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:26:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:26:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:26:41: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:26:48: 16000000 INFO @ Tue, 14 Jul 2020 10:26:54: 17000000 INFO @ Tue, 14 Jul 2020 10:26:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:27:01: 18000000 INFO @ Tue, 14 Jul 2020 10:27:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:27:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:27:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.10_summits.bed INFO @ Tue, 14 Jul 2020 10:27:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1566 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:27:08: 19000000 INFO @ Tue, 14 Jul 2020 10:27:14: 20000000 INFO @ Tue, 14 Jul 2020 10:27:21: 21000000 INFO @ Tue, 14 Jul 2020 10:27:24: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 10:27:24: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 10:27:24: #1 total tags in treatment: 8639564 INFO @ Tue, 14 Jul 2020 10:27:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:27:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:27:24: #1 tags after filtering in treatment: 8219308 INFO @ Tue, 14 Jul 2020 10:27:24: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 10:27:24: #1 finished! INFO @ Tue, 14 Jul 2020 10:27:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:27:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:27:24: #2 number of paired peaks: 247 WARNING @ Tue, 14 Jul 2020 10:27:24: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 14 Jul 2020 10:27:24: start model_add_line... INFO @ Tue, 14 Jul 2020 10:27:24: start X-correlation... INFO @ Tue, 14 Jul 2020 10:27:24: end of X-cor INFO @ Tue, 14 Jul 2020 10:27:24: #2 finished! INFO @ Tue, 14 Jul 2020 10:27:24: #2 predicted fragment length is 159 bps INFO @ Tue, 14 Jul 2020 10:27:24: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 14 Jul 2020 10:27:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.20_model.r WARNING @ Tue, 14 Jul 2020 10:27:24: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:27:24: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Tue, 14 Jul 2020 10:27:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:27:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:27:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:27:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:27:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:27:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:27:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7975016/SRX7975016.20_summits.bed INFO @ Tue, 14 Jul 2020 10:27:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (570 records, 4 fields): 1 millis CompletedMACS2peakCalling