Job ID = 14170370 SRX = SRX9720905 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26709476 spots for SRR13291895/SRR13291895.sra Written 26709476 spots for SRR13291895/SRR13291895.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170778 ("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: 00:10:15 26709476 reads; of these: 26709476 (100.00%) were unpaired; of these: 982925 (3.68%) aligned 0 times 17213704 (64.45%) aligned exactly 1 time 8512847 (31.87%) aligned >1 times 96.32% overall alignment rate Time searching: 00:10:16 Overall time: 00:10:16 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 12 files... [bam_rmdupse_core] 3357164 / 25726551 = 0.1305 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 06:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.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 06:40:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:53: 1000000 INFO @ Sat, 11 Dec 2021 06:41:01: 2000000 INFO @ Sat, 11 Dec 2021 06:41:07: 3000000 INFO @ Sat, 11 Dec 2021 06:41:13: 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 06:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.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 06:41:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:41:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:41:20: 5000000 INFO @ Sat, 11 Dec 2021 06:41:23: 1000000 INFO @ Sat, 11 Dec 2021 06:41:27: 6000000 INFO @ Sat, 11 Dec 2021 06:41:29: 2000000 INFO @ Sat, 11 Dec 2021 06:41:34: 7000000 INFO @ Sat, 11 Dec 2021 06:41:36: 3000000 INFO @ Sat, 11 Dec 2021 06:41:41: 8000000 INFO @ Sat, 11 Dec 2021 06:41:43: 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 06:41:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.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 06:41:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:41:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:41:49: 9000000 INFO @ Sat, 11 Dec 2021 06:41:49: 5000000 INFO @ Sat, 11 Dec 2021 06:41:53: 1000000 INFO @ Sat, 11 Dec 2021 06:41:56: 6000000 INFO @ Sat, 11 Dec 2021 06:41:56: 10000000 INFO @ Sat, 11 Dec 2021 06:41:59: 2000000 INFO @ Sat, 11 Dec 2021 06:42:03: 7000000 INFO @ Sat, 11 Dec 2021 06:42:04: 11000000 INFO @ Sat, 11 Dec 2021 06:42:06: 3000000 INFO @ Sat, 11 Dec 2021 06:42:10: 8000000 INFO @ Sat, 11 Dec 2021 06:42:11: 12000000 INFO @ Sat, 11 Dec 2021 06:42:13: 4000000 INFO @ Sat, 11 Dec 2021 06:42:17: 9000000 INFO @ Sat, 11 Dec 2021 06:42:18: 13000000 INFO @ Sat, 11 Dec 2021 06:42:20: 5000000 INFO @ Sat, 11 Dec 2021 06:42:23: 10000000 INFO @ Sat, 11 Dec 2021 06:42:26: 14000000 INFO @ Sat, 11 Dec 2021 06:42:26: 6000000 INFO @ Sat, 11 Dec 2021 06:42:30: 11000000 INFO @ Sat, 11 Dec 2021 06:42:33: 7000000 INFO @ Sat, 11 Dec 2021 06:42:33: 15000000 INFO @ Sat, 11 Dec 2021 06:42:37: 12000000 INFO @ Sat, 11 Dec 2021 06:42:40: 8000000 INFO @ Sat, 11 Dec 2021 06:42:41: 16000000 INFO @ Sat, 11 Dec 2021 06:42:44: 13000000 INFO @ Sat, 11 Dec 2021 06:42:47: 9000000 INFO @ Sat, 11 Dec 2021 06:42:48: 17000000 INFO @ Sat, 11 Dec 2021 06:42:51: 14000000 INFO @ Sat, 11 Dec 2021 06:42:54: 10000000 INFO @ Sat, 11 Dec 2021 06:42:56: 18000000 INFO @ Sat, 11 Dec 2021 06:42:58: 15000000 INFO @ Sat, 11 Dec 2021 06:43:01: 11000000 INFO @ Sat, 11 Dec 2021 06:43:03: 19000000 INFO @ Sat, 11 Dec 2021 06:43:05: 16000000 INFO @ Sat, 11 Dec 2021 06:43:07: 12000000 INFO @ Sat, 11 Dec 2021 06:43:10: 20000000 INFO @ Sat, 11 Dec 2021 06:43:12: 17000000 INFO @ Sat, 11 Dec 2021 06:43:14: 13000000 INFO @ Sat, 11 Dec 2021 06:43:18: 21000000 INFO @ Sat, 11 Dec 2021 06:43:19: 18000000 INFO @ Sat, 11 Dec 2021 06:43:22: 14000000 INFO @ Sat, 11 Dec 2021 06:43:25: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:43:26: 19000000 INFO @ Sat, 11 Dec 2021 06:43:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:43:28: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:43:28: #1 total tags in treatment: 22369387 INFO @ Sat, 11 Dec 2021 06:43:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:43:28: #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 06:43:28: #1 tags after filtering in treatment: 22369387 INFO @ Sat, 11 Dec 2021 06:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:43:28: #1 finished! INFO @ Sat, 11 Dec 2021 06:43:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:43:29: 15000000 INFO @ Sat, 11 Dec 2021 06:43:30: #2 number of paired peaks: 354 WARNING @ Sat, 11 Dec 2021 06:43:30: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Sat, 11 Dec 2021 06:43:30: start model_add_line... INFO @ Sat, 11 Dec 2021 06:43:30: start X-correlation... INFO @ Sat, 11 Dec 2021 06:43:30: end of X-cor INFO @ Sat, 11 Dec 2021 06:43:30: #2 finished! INFO @ Sat, 11 Dec 2021 06:43:30: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 06:43:30: #2 alternative fragment length(s) may be 1,48,538 bps INFO @ Sat, 11 Dec 2021 06:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.05_model.r WARNING @ Sat, 11 Dec 2021 06:43:30: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:43:30: #2 You may need to consider one of the other alternative d(s): 1,48,538 WARNING @ Sat, 11 Dec 2021 06:43:30: #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 06:43:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:43:33: 20000000 INFO @ Sat, 11 Dec 2021 06:43:36: 16000000 INFO @ Sat, 11 Dec 2021 06:43:41: 21000000 INFO @ Sat, 11 Dec 2021 06:43:43: 17000000 INFO @ Sat, 11 Dec 2021 06:43:48: 22000000 INFO @ Sat, 11 Dec 2021 06:43:50: 18000000 INFO @ Sat, 11 Dec 2021 06:43:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:43:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:43:51: #1 total tags in treatment: 22369387 INFO @ Sat, 11 Dec 2021 06:43:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:43:51: #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 06:43:51: #1 tags after filtering in treatment: 22369387 INFO @ Sat, 11 Dec 2021 06:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:43:51: #1 finished! INFO @ Sat, 11 Dec 2021 06:43:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:43:52: #2 number of paired peaks: 354 WARNING @ Sat, 11 Dec 2021 06:43:52: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Sat, 11 Dec 2021 06:43:52: start model_add_line... INFO @ Sat, 11 Dec 2021 06:43:53: start X-correlation... INFO @ Sat, 11 Dec 2021 06:43:53: end of X-cor INFO @ Sat, 11 Dec 2021 06:43:53: #2 finished! INFO @ Sat, 11 Dec 2021 06:43:53: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 06:43:53: #2 alternative fragment length(s) may be 1,48,538 bps INFO @ Sat, 11 Dec 2021 06:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.10_model.r WARNING @ Sat, 11 Dec 2021 06:43:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:43:53: #2 You may need to consider one of the other alternative d(s): 1,48,538 WARNING @ Sat, 11 Dec 2021 06:43:53: #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 06:43:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:43:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:43:56: 19000000 INFO @ Sat, 11 Dec 2021 06:44:02: 20000000 INFO @ Sat, 11 Dec 2021 06:44:08: 21000000 INFO @ Sat, 11 Dec 2021 06:44:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:44:15: 22000000 INFO @ Sat, 11 Dec 2021 06:44:17: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:44:17: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:44:17: #1 total tags in treatment: 22369387 INFO @ Sat, 11 Dec 2021 06:44:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:44:17: #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 06:44:17: #1 tags after filtering in treatment: 22369387 INFO @ Sat, 11 Dec 2021 06:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:44:17: #1 finished! INFO @ Sat, 11 Dec 2021 06:44:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:44:19: #2 number of paired peaks: 354 WARNING @ Sat, 11 Dec 2021 06:44:19: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Sat, 11 Dec 2021 06:44:19: start model_add_line... INFO @ Sat, 11 Dec 2021 06:44:19: start X-correlation... INFO @ Sat, 11 Dec 2021 06:44:19: end of X-cor INFO @ Sat, 11 Dec 2021 06:44:19: #2 finished! INFO @ Sat, 11 Dec 2021 06:44:19: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 06:44:19: #2 alternative fragment length(s) may be 1,48,538 bps INFO @ Sat, 11 Dec 2021 06:44:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.20_model.r WARNING @ Sat, 11 Dec 2021 06:44:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:44:19: #2 You may need to consider one of the other alternative d(s): 1,48,538 WARNING @ Sat, 11 Dec 2021 06:44:19: #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 06:44:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:44:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:44:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:44:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.05_summits.bed INFO @ Sat, 11 Dec 2021 06:44:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3286 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:44:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:44:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:44:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:44:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.10_summits.bed INFO @ Sat, 11 Dec 2021 06:44:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1954 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:44:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:45:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:45:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:45:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720905/SRX9720905.20_summits.bed INFO @ Sat, 11 Dec 2021 06:45:16: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (663 records, 4 fields): 2 millis CompletedMACS2peakCalling