Job ID = 14171564 SRX = SRX2765812 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 40869305 spots for SRR5482399/SRR5482399.sra Written 40869305 spots for SRR5482399/SRR5482399.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172076 ("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: 00:18:42 40869305 reads; of these: 40869305 (100.00%) were unpaired; of these: 2612405 (6.39%) aligned 0 times 24316767 (59.50%) aligned exactly 1 time 13940133 (34.11%) aligned >1 times 93.61% overall alignment rate Time searching: 00:18:42 Overall time: 00:18:42 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_rmdupse_core] 7917318 / 38256900 = 0.2070 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 12:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.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 12:36:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:36:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:36:41: 1000000 INFO @ Sat, 11 Dec 2021 12:36:51: 2000000 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 12:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.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 12:37:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:37:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:37:01: 3000000 INFO @ Sat, 11 Dec 2021 12:37:09: 1000000 INFO @ Sat, 11 Dec 2021 12:37:10: 4000000 INFO @ Sat, 11 Dec 2021 12:37:18: 2000000 INFO @ Sat, 11 Dec 2021 12:37:21: 5000000 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 12:37:27: 3000000 INFO @ Sat, 11 Dec 2021 12:37:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.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 12:37:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:37:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:37:31: 6000000 INFO @ Sat, 11 Dec 2021 12:37:37: 4000000 INFO @ Sat, 11 Dec 2021 12:37:39: 1000000 INFO @ Sat, 11 Dec 2021 12:37:41: 7000000 INFO @ Sat, 11 Dec 2021 12:37:46: 5000000 INFO @ Sat, 11 Dec 2021 12:37:49: 2000000 INFO @ Sat, 11 Dec 2021 12:37:51: 8000000 INFO @ Sat, 11 Dec 2021 12:37:55: 6000000 INFO @ Sat, 11 Dec 2021 12:37:59: 3000000 INFO @ Sat, 11 Dec 2021 12:38:01: 9000000 INFO @ Sat, 11 Dec 2021 12:38:05: 7000000 INFO @ Sat, 11 Dec 2021 12:38:08: 4000000 INFO @ Sat, 11 Dec 2021 12:38:11: 10000000 INFO @ Sat, 11 Dec 2021 12:38:14: 8000000 INFO @ Sat, 11 Dec 2021 12:38:18: 5000000 INFO @ Sat, 11 Dec 2021 12:38:22: 11000000 INFO @ Sat, 11 Dec 2021 12:38:24: 9000000 INFO @ Sat, 11 Dec 2021 12:38:27: 6000000 INFO @ Sat, 11 Dec 2021 12:38:32: 12000000 INFO @ Sat, 11 Dec 2021 12:38:33: 10000000 INFO @ Sat, 11 Dec 2021 12:38:36: 7000000 INFO @ Sat, 11 Dec 2021 12:38:42: 13000000 INFO @ Sat, 11 Dec 2021 12:38:43: 11000000 INFO @ Sat, 11 Dec 2021 12:38:46: 8000000 INFO @ Sat, 11 Dec 2021 12:38:51: 14000000 INFO @ Sat, 11 Dec 2021 12:38:52: 12000000 INFO @ Sat, 11 Dec 2021 12:38:55: 9000000 INFO @ Sat, 11 Dec 2021 12:39:01: 13000000 INFO @ Sat, 11 Dec 2021 12:39:01: 15000000 INFO @ Sat, 11 Dec 2021 12:39:04: 10000000 INFO @ Sat, 11 Dec 2021 12:39:10: 14000000 INFO @ Sat, 11 Dec 2021 12:39:11: 16000000 INFO @ Sat, 11 Dec 2021 12:39:13: 11000000 INFO @ Sat, 11 Dec 2021 12:39:19: 15000000 INFO @ Sat, 11 Dec 2021 12:39:22: 17000000 INFO @ Sat, 11 Dec 2021 12:39:22: 12000000 INFO @ Sat, 11 Dec 2021 12:39:28: 16000000 INFO @ Sat, 11 Dec 2021 12:39:31: 13000000 INFO @ Sat, 11 Dec 2021 12:39:32: 18000000 INFO @ Sat, 11 Dec 2021 12:39:37: 17000000 INFO @ Sat, 11 Dec 2021 12:39:40: 14000000 INFO @ Sat, 11 Dec 2021 12:39:42: 19000000 INFO @ Sat, 11 Dec 2021 12:39:46: 18000000 INFO @ Sat, 11 Dec 2021 12:39:49: 15000000 INFO @ Sat, 11 Dec 2021 12:39:53: 20000000 INFO @ Sat, 11 Dec 2021 12:39:54: 19000000 INFO @ Sat, 11 Dec 2021 12:39:57: 16000000 INFO @ Sat, 11 Dec 2021 12:40:03: 20000000 INFO @ Sat, 11 Dec 2021 12:40:03: 21000000 INFO @ Sat, 11 Dec 2021 12:40:06: 17000000 INFO @ Sat, 11 Dec 2021 12:40:12: 21000000 INFO @ Sat, 11 Dec 2021 12:40:13: 22000000 INFO @ Sat, 11 Dec 2021 12:40:15: 18000000 INFO @ Sat, 11 Dec 2021 12:40:21: 22000000 INFO @ Sat, 11 Dec 2021 12:40:24: 23000000 INFO @ Sat, 11 Dec 2021 12:40:24: 19000000 INFO @ Sat, 11 Dec 2021 12:40:30: 23000000 INFO @ Sat, 11 Dec 2021 12:40:33: 20000000 INFO @ Sat, 11 Dec 2021 12:40:34: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:40:38: 24000000 INFO @ Sat, 11 Dec 2021 12:40:42: 21000000 INFO @ Sat, 11 Dec 2021 12:40:44: 25000000 INFO @ Sat, 11 Dec 2021 12:40:47: 25000000 INFO @ Sat, 11 Dec 2021 12:40:51: 22000000 INFO @ Sat, 11 Dec 2021 12:40:54: 26000000 INFO @ Sat, 11 Dec 2021 12:40:56: 26000000 INFO @ Sat, 11 Dec 2021 12:40:59: 23000000 INFO @ Sat, 11 Dec 2021 12:41:04: 27000000 INFO @ Sat, 11 Dec 2021 12:41:04: 27000000 INFO @ Sat, 11 Dec 2021 12:41:08: 24000000 INFO @ Sat, 11 Dec 2021 12:41:13: 28000000 INFO @ Sat, 11 Dec 2021 12:41:15: 28000000 INFO @ Sat, 11 Dec 2021 12:41:17: 25000000 INFO @ Sat, 11 Dec 2021 12:41:23: 29000000 INFO @ Sat, 11 Dec 2021 12:41:25: 29000000 INFO @ Sat, 11 Dec 2021 12:41:26: 26000000 INFO @ Sat, 11 Dec 2021 12:41:32: 30000000 INFO @ Sat, 11 Dec 2021 12:41:35: 30000000 INFO @ Sat, 11 Dec 2021 12:41:35: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:41:35: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:41:35: #1 total tags in treatment: 30339582 INFO @ Sat, 11 Dec 2021 12:41:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:41:35: #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 12:41:35: 27000000 INFO @ Sat, 11 Dec 2021 12:41:36: #1 tags after filtering in treatment: 30339582 INFO @ Sat, 11 Dec 2021 12:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:41:36: #1 finished! INFO @ Sat, 11 Dec 2021 12:41:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:41:38: #2 number of paired peaks: 383 WARNING @ Sat, 11 Dec 2021 12:41:38: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Sat, 11 Dec 2021 12:41:38: start model_add_line... INFO @ Sat, 11 Dec 2021 12:41:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:41:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:41:38: #1 total tags in treatment: 30339582 INFO @ Sat, 11 Dec 2021 12:41:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:41:38: #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 12:41:38: start X-correlation... INFO @ Sat, 11 Dec 2021 12:41:39: end of X-cor INFO @ Sat, 11 Dec 2021 12:41:39: #2 finished! INFO @ Sat, 11 Dec 2021 12:41:39: #2 predicted fragment length is 2 bps INFO @ Sat, 11 Dec 2021 12:41:39: #2 alternative fragment length(s) may be 2,27,50,567 bps INFO @ Sat, 11 Dec 2021 12:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10_model.r WARNING @ Sat, 11 Dec 2021 12:41:39: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:41:39: #2 You may need to consider one of the other alternative d(s): 2,27,50,567 WARNING @ Sat, 11 Dec 2021 12:41:39: #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 12:41:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:41:39: #1 tags after filtering in treatment: 30339582 INFO @ Sat, 11 Dec 2021 12:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:41:39: #1 finished! INFO @ Sat, 11 Dec 2021 12:41:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:41:42: #2 number of paired peaks: 383 WARNING @ Sat, 11 Dec 2021 12:41:42: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Sat, 11 Dec 2021 12:41:42: start model_add_line... INFO @ Sat, 11 Dec 2021 12:41:42: start X-correlation... INFO @ Sat, 11 Dec 2021 12:41:42: end of X-cor INFO @ Sat, 11 Dec 2021 12:41:42: #2 finished! INFO @ Sat, 11 Dec 2021 12:41:42: #2 predicted fragment length is 2 bps INFO @ Sat, 11 Dec 2021 12:41:42: #2 alternative fragment length(s) may be 2,27,50,567 bps INFO @ Sat, 11 Dec 2021 12:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05_model.r WARNING @ Sat, 11 Dec 2021 12:41:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:41:42: #2 You may need to consider one of the other alternative d(s): 2,27,50,567 WARNING @ Sat, 11 Dec 2021 12:41:42: #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 12:41:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:41:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:41:44: 28000000 INFO @ Sat, 11 Dec 2021 12:41:52: 29000000 INFO @ Sat, 11 Dec 2021 12:42:01: 30000000 INFO @ Sat, 11 Dec 2021 12:42:04: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:42:04: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:42:04: #1 total tags in treatment: 30339582 INFO @ Sat, 11 Dec 2021 12:42:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:42:04: #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 12:42:04: #1 tags after filtering in treatment: 30339582 INFO @ Sat, 11 Dec 2021 12:42:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:42:04: #1 finished! INFO @ Sat, 11 Dec 2021 12:42:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:42:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:42:07: #2 number of paired peaks: 383 WARNING @ Sat, 11 Dec 2021 12:42:07: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Sat, 11 Dec 2021 12:42:07: start model_add_line... INFO @ Sat, 11 Dec 2021 12:42:07: start X-correlation... INFO @ Sat, 11 Dec 2021 12:42:07: end of X-cor INFO @ Sat, 11 Dec 2021 12:42:07: #2 finished! INFO @ Sat, 11 Dec 2021 12:42:07: #2 predicted fragment length is 2 bps INFO @ Sat, 11 Dec 2021 12:42:07: #2 alternative fragment length(s) may be 2,27,50,567 bps INFO @ Sat, 11 Dec 2021 12:42:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20_model.r WARNING @ Sat, 11 Dec 2021 12:42:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:42:07: #2 You may need to consider one of the other alternative d(s): 2,27,50,567 WARNING @ Sat, 11 Dec 2021 12:42:07: #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 12:42:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:42:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:42:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:42:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:43:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:43:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:43:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:43:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10_summits.bed INFO @ Sat, 11 Dec 2021 12:43:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:43:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05_summits.bed INFO @ Sat, 11 Dec 2021 12:43:17: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:43:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:43:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20_summits.bed INFO @ Sat, 11 Dec 2021 12:43:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling