Job ID = 14170602 SRX = SRX8497056 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15767405 spots for SRR11952655/SRR11952655.sra Written 15767405 spots for SRR11952655/SRR11952655.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171169 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:53:41 15767405 reads; of these: 15767405 (100.00%) were paired; of these: 1732971 (10.99%) aligned concordantly 0 times 9841575 (62.42%) aligned concordantly exactly 1 time 4192859 (26.59%) aligned concordantly >1 times ---- 1732971 pairs aligned concordantly 0 times; of these: 407646 (23.52%) aligned discordantly 1 time ---- 1325325 pairs aligned 0 times concordantly or discordantly; of these: 2650650 mates make up the pairs; of these: 1778112 (67.08%) aligned 0 times 394465 (14.88%) aligned exactly 1 time 478073 (18.04%) aligned >1 times 94.36% overall alignment rate Time searching: 00:53:42 Overall time: 00:53:42 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 16 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] 926237 / 14377611 = 0.0644 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 08:32:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.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 08:32:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:32:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:32:53: 1000000 INFO @ Sat, 11 Dec 2021 08:33:01: 2000000 INFO @ Sat, 11 Dec 2021 08:33:09: 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 08:33:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.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 08:33:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:33:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:33:18: 4000000 INFO @ Sat, 11 Dec 2021 08:33:24: 1000000 INFO @ Sat, 11 Dec 2021 08:33:27: 5000000 INFO @ Sat, 11 Dec 2021 08:33:33: 2000000 INFO @ Sat, 11 Dec 2021 08:33:36: 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 @ Sat, 11 Dec 2021 08:33:42: 3000000 INFO @ Sat, 11 Dec 2021 08:33:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.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 08:33:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:33:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:33:45: 7000000 INFO @ Sat, 11 Dec 2021 08:33:52: 4000000 INFO @ Sat, 11 Dec 2021 08:33:55: 8000000 INFO @ Sat, 11 Dec 2021 08:33:58: 1000000 INFO @ Sat, 11 Dec 2021 08:34:02: 5000000 INFO @ Sat, 11 Dec 2021 08:34:05: 9000000 INFO @ Sat, 11 Dec 2021 08:34:11: 2000000 INFO @ Sat, 11 Dec 2021 08:34:12: 6000000 INFO @ Sat, 11 Dec 2021 08:34:15: 10000000 INFO @ Sat, 11 Dec 2021 08:34:22: 7000000 INFO @ Sat, 11 Dec 2021 08:34:24: 3000000 INFO @ Sat, 11 Dec 2021 08:34:24: 11000000 INFO @ Sat, 11 Dec 2021 08:34:31: 8000000 INFO @ Sat, 11 Dec 2021 08:34:34: 12000000 INFO @ Sat, 11 Dec 2021 08:34:37: 4000000 INFO @ Sat, 11 Dec 2021 08:34:41: 9000000 INFO @ Sat, 11 Dec 2021 08:34:43: 13000000 INFO @ Sat, 11 Dec 2021 08:34:50: 5000000 INFO @ Sat, 11 Dec 2021 08:34:51: 10000000 INFO @ Sat, 11 Dec 2021 08:34:53: 14000000 INFO @ Sat, 11 Dec 2021 08:35:01: 11000000 INFO @ Sat, 11 Dec 2021 08:35:03: 15000000 INFO @ Sat, 11 Dec 2021 08:35:03: 6000000 INFO @ Sat, 11 Dec 2021 08:35:10: 12000000 INFO @ Sat, 11 Dec 2021 08:35:13: 16000000 INFO @ Sat, 11 Dec 2021 08:35:17: 7000000 INFO @ Sat, 11 Dec 2021 08:35:20: 13000000 INFO @ Sat, 11 Dec 2021 08:35:22: 17000000 INFO @ Sat, 11 Dec 2021 08:35:30: 14000000 INFO @ Sat, 11 Dec 2021 08:35:30: 8000000 INFO @ Sat, 11 Dec 2021 08:35:32: 18000000 INFO @ Sat, 11 Dec 2021 08:35:39: 15000000 INFO @ Sat, 11 Dec 2021 08:35:41: 19000000 INFO @ Sat, 11 Dec 2021 08:35:43: 9000000 INFO @ Sat, 11 Dec 2021 08:35:49: 16000000 INFO @ Sat, 11 Dec 2021 08:35:51: 20000000 INFO @ Sat, 11 Dec 2021 08:35:56: 10000000 INFO @ Sat, 11 Dec 2021 08:35:58: 17000000 INFO @ Sat, 11 Dec 2021 08:36:00: 21000000 INFO @ Sat, 11 Dec 2021 08:36:08: 18000000 INFO @ Sat, 11 Dec 2021 08:36:08: 11000000 INFO @ Sat, 11 Dec 2021 08:36:10: 22000000 INFO @ Sat, 11 Dec 2021 08:36:18: 19000000 INFO @ Sat, 11 Dec 2021 08:36:20: 23000000 INFO @ Sat, 11 Dec 2021 08:36:21: 12000000 INFO @ Sat, 11 Dec 2021 08:36:27: 20000000 INFO @ Sat, 11 Dec 2021 08:36:30: 24000000 INFO @ Sat, 11 Dec 2021 08:36:34: 13000000 INFO @ Sat, 11 Dec 2021 08:36:37: 21000000 INFO @ Sat, 11 Dec 2021 08:36:39: 25000000 INFO @ Sat, 11 Dec 2021 08:36:47: 22000000 INFO @ Sat, 11 Dec 2021 08:36:47: 14000000 INFO @ Sat, 11 Dec 2021 08:36:49: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:36:56: 23000000 INFO @ Sat, 11 Dec 2021 08:36:59: 27000000 INFO @ Sat, 11 Dec 2021 08:37:00: 15000000 INFO @ Sat, 11 Dec 2021 08:37:06: 24000000 INFO @ Sat, 11 Dec 2021 08:37:07: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:37:07: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:37:07: #1 total tags in treatment: 13124758 INFO @ Sat, 11 Dec 2021 08:37:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:37:07: #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 08:37:07: #1 tags after filtering in treatment: 12192434 INFO @ Sat, 11 Dec 2021 08:37:07: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 08:37:07: #1 finished! INFO @ Sat, 11 Dec 2021 08:37:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:37:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:37:08: #2 number of paired peaks: 205 WARNING @ Sat, 11 Dec 2021 08:37:08: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sat, 11 Dec 2021 08:37:08: start model_add_line... INFO @ Sat, 11 Dec 2021 08:37:08: start X-correlation... INFO @ Sat, 11 Dec 2021 08:37:08: end of X-cor INFO @ Sat, 11 Dec 2021 08:37:08: #2 finished! INFO @ Sat, 11 Dec 2021 08:37:08: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 08:37:08: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 08:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.05_model.r WARNING @ Sat, 11 Dec 2021 08:37:08: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:37:08: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 08:37:08: #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 08:37:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:37:13: 16000000 INFO @ Sat, 11 Dec 2021 08:37:15: 25000000 INFO @ Sat, 11 Dec 2021 08:37:23: 26000000 INFO @ Sat, 11 Dec 2021 08:37:26: 17000000 INFO @ Sat, 11 Dec 2021 08:37:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:37:32: 27000000 INFO @ Sat, 11 Dec 2021 08:37:39: 18000000 INFO @ Sat, 11 Dec 2021 08:37:39: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:37:39: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:37:39: #1 total tags in treatment: 13124758 INFO @ Sat, 11 Dec 2021 08:37:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:37:39: #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 08:37:40: #1 tags after filtering in treatment: 12192434 INFO @ Sat, 11 Dec 2021 08:37:40: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 08:37:40: #1 finished! INFO @ Sat, 11 Dec 2021 08:37:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:37:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:37:40: #2 number of paired peaks: 205 WARNING @ Sat, 11 Dec 2021 08:37:40: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sat, 11 Dec 2021 08:37:40: start model_add_line... INFO @ Sat, 11 Dec 2021 08:37:40: start X-correlation... INFO @ Sat, 11 Dec 2021 08:37:40: end of X-cor INFO @ Sat, 11 Dec 2021 08:37:40: #2 finished! INFO @ Sat, 11 Dec 2021 08:37:40: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 08:37:40: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 08:37:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.10_model.r WARNING @ Sat, 11 Dec 2021 08:37:40: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:37:40: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 08:37:40: #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 08:37:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:37:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:37:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:37:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:37:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.05_summits.bed INFO @ Sat, 11 Dec 2021 08:37:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1810 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:37:51: 19000000 INFO @ Sat, 11 Dec 2021 08:38:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:38:03: 20000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:38:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:38:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:38:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.10_summits.bed INFO @ Sat, 11 Dec 2021 08:38:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1001 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:38:16: 21000000 INFO @ Sat, 11 Dec 2021 08:38:30: 22000000 INFO @ Sat, 11 Dec 2021 08:38:43: 23000000 INFO @ Sat, 11 Dec 2021 08:38:56: 24000000 INFO @ Sat, 11 Dec 2021 08:39:10: 25000000 INFO @ Sat, 11 Dec 2021 08:39:25: 26000000 INFO @ Sat, 11 Dec 2021 08:39:40: 27000000 INFO @ Sat, 11 Dec 2021 08:39:52: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:39:52: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:39:52: #1 total tags in treatment: 13124758 INFO @ Sat, 11 Dec 2021 08:39:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:39:52: #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 08:39:52: #1 tags after filtering in treatment: 12192434 INFO @ Sat, 11 Dec 2021 08:39:52: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 08:39:52: #1 finished! INFO @ Sat, 11 Dec 2021 08:39:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:39:53: #2 number of paired peaks: 205 WARNING @ Sat, 11 Dec 2021 08:39:53: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sat, 11 Dec 2021 08:39:53: start model_add_line... INFO @ Sat, 11 Dec 2021 08:39:53: start X-correlation... INFO @ Sat, 11 Dec 2021 08:39:53: end of X-cor INFO @ Sat, 11 Dec 2021 08:39:53: #2 finished! INFO @ Sat, 11 Dec 2021 08:39:53: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 08:39:53: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 08:39:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.20_model.r WARNING @ Sat, 11 Dec 2021 08:39:53: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:39:53: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 08:39:53: #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 08:39:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:39:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:40:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497056/SRX8497056.20_summits.bed INFO @ Sat, 11 Dec 2021 08:40:29: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (475 records, 4 fields): 2 millis CompletedMACS2peakCalling