Job ID = 14171548 SRX = SRX2765811 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 41952663 spots for SRR5482398/SRR5482398.sra Written 41952663 spots for SRR5482398/SRR5482398.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172062 ("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: 00:17:39 41952663 reads; of these: 41952663 (100.00%) were unpaired; of these: 6783654 (16.17%) aligned 0 times 21344625 (50.88%) aligned exactly 1 time 13824384 (32.95%) aligned >1 times 83.83% overall alignment rate Time searching: 00:17:39 Overall time: 00:17:39 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] 6917396 / 35169009 = 0.1967 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 12:29:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.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 12:29:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:29:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:29:59: 1000000 INFO @ Sat, 11 Dec 2021 12:30:05: 2000000 INFO @ Sat, 11 Dec 2021 12:30:11: 3000000 INFO @ Sat, 11 Dec 2021 12:30:18: 4000000 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 12:30:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.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 12:30:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:30:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:30:24: 5000000 INFO @ Sat, 11 Dec 2021 12:30:28: 1000000 INFO @ Sat, 11 Dec 2021 12:30:31: 6000000 INFO @ Sat, 11 Dec 2021 12:30:34: 2000000 INFO @ Sat, 11 Dec 2021 12:30:37: 7000000 INFO @ Sat, 11 Dec 2021 12:30:40: 3000000 INFO @ Sat, 11 Dec 2021 12:30:43: 8000000 INFO @ Sat, 11 Dec 2021 12:30:46: 4000000 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 12:30:50: 9000000 INFO @ Sat, 11 Dec 2021 12:30:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.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 12:30:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:30:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:30:53: 5000000 INFO @ Sat, 11 Dec 2021 12:30:56: 10000000 INFO @ Sat, 11 Dec 2021 12:30:59: 1000000 INFO @ Sat, 11 Dec 2021 12:31:00: 6000000 INFO @ Sat, 11 Dec 2021 12:31:03: 11000000 INFO @ Sat, 11 Dec 2021 12:31:06: 2000000 INFO @ Sat, 11 Dec 2021 12:31:07: 7000000 INFO @ Sat, 11 Dec 2021 12:31:09: 12000000 INFO @ Sat, 11 Dec 2021 12:31:12: 3000000 INFO @ Sat, 11 Dec 2021 12:31:15: 8000000 INFO @ Sat, 11 Dec 2021 12:31:16: 13000000 INFO @ Sat, 11 Dec 2021 12:31:18: 4000000 INFO @ Sat, 11 Dec 2021 12:31:22: 14000000 INFO @ Sat, 11 Dec 2021 12:31:22: 9000000 INFO @ Sat, 11 Dec 2021 12:31:25: 5000000 INFO @ Sat, 11 Dec 2021 12:31:28: 15000000 INFO @ Sat, 11 Dec 2021 12:31:30: 10000000 INFO @ Sat, 11 Dec 2021 12:31:32: 6000000 INFO @ Sat, 11 Dec 2021 12:31:35: 16000000 INFO @ Sat, 11 Dec 2021 12:31:37: 11000000 INFO @ Sat, 11 Dec 2021 12:31:40: 7000000 INFO @ Sat, 11 Dec 2021 12:31:41: 17000000 INFO @ Sat, 11 Dec 2021 12:31:44: 12000000 INFO @ Sat, 11 Dec 2021 12:31:47: 8000000 INFO @ Sat, 11 Dec 2021 12:31:48: 18000000 INFO @ Sat, 11 Dec 2021 12:31:51: 13000000 INFO @ Sat, 11 Dec 2021 12:31:54: 19000000 INFO @ Sat, 11 Dec 2021 12:31:54: 9000000 INFO @ Sat, 11 Dec 2021 12:31:58: 14000000 INFO @ Sat, 11 Dec 2021 12:32:01: 20000000 INFO @ Sat, 11 Dec 2021 12:32:01: 10000000 INFO @ Sat, 11 Dec 2021 12:32:05: 15000000 INFO @ Sat, 11 Dec 2021 12:32:07: 21000000 INFO @ Sat, 11 Dec 2021 12:32:09: 11000000 INFO @ Sat, 11 Dec 2021 12:32:12: 16000000 INFO @ Sat, 11 Dec 2021 12:32:13: 22000000 INFO @ Sat, 11 Dec 2021 12:32:16: 12000000 INFO @ Sat, 11 Dec 2021 12:32:19: 17000000 INFO @ Sat, 11 Dec 2021 12:32:20: 23000000 INFO @ Sat, 11 Dec 2021 12:32:22: 13000000 INFO @ Sat, 11 Dec 2021 12:32:26: 18000000 INFO @ Sat, 11 Dec 2021 12:32:26: 24000000 INFO @ Sat, 11 Dec 2021 12:32:29: 14000000 INFO @ Sat, 11 Dec 2021 12:32:32: 25000000 INFO @ Sat, 11 Dec 2021 12:32:33: 19000000 INFO @ Sat, 11 Dec 2021 12:32:36: 15000000 INFO @ Sat, 11 Dec 2021 12:32:39: 26000000 INFO @ Sat, 11 Dec 2021 12:32:39: 20000000 INFO @ Sat, 11 Dec 2021 12:32:44: 16000000 INFO @ Sat, 11 Dec 2021 12:32:46: 27000000 INFO @ Sat, 11 Dec 2021 12:32:46: 21000000 INFO @ Sat, 11 Dec 2021 12:32:51: 17000000 INFO @ Sat, 11 Dec 2021 12:32:52: 28000000 INFO @ Sat, 11 Dec 2021 12:32:53: 22000000 INFO @ Sat, 11 Dec 2021 12:32:54: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:32:54: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:32:54: #1 total tags in treatment: 28251613 INFO @ Sat, 11 Dec 2021 12:32:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:32:54: #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 12:32:55: #1 tags after filtering in treatment: 28251613 INFO @ Sat, 11 Dec 2021 12:32:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:32:55: #1 finished! INFO @ Sat, 11 Dec 2021 12:32:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:32:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:32:57: #2 number of paired peaks: 344 WARNING @ Sat, 11 Dec 2021 12:32:57: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sat, 11 Dec 2021 12:32:57: start model_add_line... INFO @ Sat, 11 Dec 2021 12:32:57: start X-correlation... INFO @ Sat, 11 Dec 2021 12:32:57: end of X-cor INFO @ Sat, 11 Dec 2021 12:32:57: #2 finished! INFO @ Sat, 11 Dec 2021 12:32:57: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 12:32:57: #2 alternative fragment length(s) may be 1,44,562,592,598 bps INFO @ Sat, 11 Dec 2021 12:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05_model.r WARNING @ Sat, 11 Dec 2021 12:32:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:32:57: #2 You may need to consider one of the other alternative d(s): 1,44,562,592,598 WARNING @ Sat, 11 Dec 2021 12:32:57: #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 12:32:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:32:58: 18000000 INFO @ Sat, 11 Dec 2021 12:33:00: 23000000 INFO @ Sat, 11 Dec 2021 12:33:05: 19000000 INFO @ Sat, 11 Dec 2021 12:33:07: 24000000 INFO @ Sat, 11 Dec 2021 12:33:13: 20000000 INFO @ Sat, 11 Dec 2021 12:33:14: 25000000 INFO @ Sat, 11 Dec 2021 12:33:19: 21000000 INFO @ Sat, 11 Dec 2021 12:33:21: 26000000 INFO @ Sat, 11 Dec 2021 12:33:26: 22000000 INFO @ Sat, 11 Dec 2021 12:33:28: 27000000 INFO @ Sat, 11 Dec 2021 12:33:33: 23000000 INFO @ Sat, 11 Dec 2021 12:33:35: 28000000 INFO @ Sat, 11 Dec 2021 12:33:37: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:33:37: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:33:37: #1 total tags in treatment: 28251613 INFO @ Sat, 11 Dec 2021 12:33:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:33:37: #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 12:33:37: #1 tags after filtering in treatment: 28251613 INFO @ Sat, 11 Dec 2021 12:33:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:33:37: #1 finished! INFO @ Sat, 11 Dec 2021 12:33:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:33:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:33:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:33:39: #2 number of paired peaks: 344 WARNING @ Sat, 11 Dec 2021 12:33:39: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sat, 11 Dec 2021 12:33:39: start model_add_line... INFO @ Sat, 11 Dec 2021 12:33:40: start X-correlation... INFO @ Sat, 11 Dec 2021 12:33:40: end of X-cor INFO @ Sat, 11 Dec 2021 12:33:40: #2 finished! INFO @ Sat, 11 Dec 2021 12:33:40: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 12:33:40: #2 alternative fragment length(s) may be 1,44,562,592,598 bps INFO @ Sat, 11 Dec 2021 12:33:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10_model.r WARNING @ Sat, 11 Dec 2021 12:33:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:33:40: #2 You may need to consider one of the other alternative d(s): 1,44,562,592,598 WARNING @ Sat, 11 Dec 2021 12:33:40: #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 12:33:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:33:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:33:40: 24000000 INFO @ Sat, 11 Dec 2021 12:33:48: 25000000 INFO @ Sat, 11 Dec 2021 12:33:54: 26000000 INFO @ Sat, 11 Dec 2021 12:34:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:34:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:34:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.05_summits.bed INFO @ Sat, 11 Dec 2021 12:34:00: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:34:01: 27000000 INFO @ Sat, 11 Dec 2021 12:34:08: 28000000 INFO @ Sat, 11 Dec 2021 12:34:10: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:34:10: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:34:10: #1 total tags in treatment: 28251613 INFO @ Sat, 11 Dec 2021 12:34:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:34:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:34:10: #1 tags after filtering in treatment: 28251613 INFO @ Sat, 11 Dec 2021 12:34:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:34:10: #1 finished! INFO @ Sat, 11 Dec 2021 12:34:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:34:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:34:12: #2 number of paired peaks: 344 WARNING @ Sat, 11 Dec 2021 12:34:12: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sat, 11 Dec 2021 12:34:12: start model_add_line... INFO @ Sat, 11 Dec 2021 12:34:12: start X-correlation... INFO @ Sat, 11 Dec 2021 12:34:12: end of X-cor INFO @ Sat, 11 Dec 2021 12:34:12: #2 finished! INFO @ Sat, 11 Dec 2021 12:34:12: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 12:34:12: #2 alternative fragment length(s) may be 1,44,562,592,598 bps INFO @ Sat, 11 Dec 2021 12:34:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20_model.r WARNING @ Sat, 11 Dec 2021 12:34:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:34:12: #2 You may need to consider one of the other alternative d(s): 1,44,562,592,598 WARNING @ Sat, 11 Dec 2021 12:34:12: #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 12:34:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:34:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.10_summits.bed INFO @ Sat, 11 Dec 2021 12:34:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:34:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765811/SRX2765811.20_summits.bed INFO @ Sat, 11 Dec 2021 12:35:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。