Job ID = 14170483 SRX = SRX8689044 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19117994 spots for SRR12174244/SRR12174244.sra Written 19117994 spots for SRR12174244/SRR12174244.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170918 ("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: 00:08:30 19117994 reads; of these: 19117994 (100.00%) were unpaired; of these: 527117 (2.76%) aligned 0 times 12004031 (62.79%) aligned exactly 1 time 6586846 (34.45%) aligned >1 times 97.24% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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 8 files... [bam_rmdupse_core] 1948564 / 18590877 = 0.1048 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 07:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.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 07:10:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:10:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:10:20: 1000000 INFO @ Sat, 11 Dec 2021 07:10:27: 2000000 INFO @ Sat, 11 Dec 2021 07:10:34: 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 07:10:41: 4000000 INFO @ Sat, 11 Dec 2021 07:10:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.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 07:10:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:10:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:10:48: 5000000 INFO @ Sat, 11 Dec 2021 07:10:50: 1000000 INFO @ Sat, 11 Dec 2021 07:10:55: 6000000 INFO @ Sat, 11 Dec 2021 07:10:58: 2000000 INFO @ Sat, 11 Dec 2021 07:11:02: 7000000 INFO @ Sat, 11 Dec 2021 07:11:05: 3000000 INFO @ Sat, 11 Dec 2021 07:11:09: 8000000 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 07:11:12: 4000000 INFO @ Sat, 11 Dec 2021 07:11:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.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 07:11:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:11:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:11:16: 9000000 INFO @ Sat, 11 Dec 2021 07:11:19: 5000000 INFO @ Sat, 11 Dec 2021 07:11:21: 1000000 INFO @ Sat, 11 Dec 2021 07:11:23: 10000000 INFO @ Sat, 11 Dec 2021 07:11:26: 6000000 INFO @ Sat, 11 Dec 2021 07:11:28: 2000000 INFO @ Sat, 11 Dec 2021 07:11:30: 11000000 INFO @ Sat, 11 Dec 2021 07:11:33: 7000000 INFO @ Sat, 11 Dec 2021 07:11:36: 3000000 INFO @ Sat, 11 Dec 2021 07:11:38: 12000000 INFO @ Sat, 11 Dec 2021 07:11:41: 8000000 INFO @ Sat, 11 Dec 2021 07:11:43: 4000000 INFO @ Sat, 11 Dec 2021 07:11:45: 13000000 INFO @ Sat, 11 Dec 2021 07:11:48: 9000000 INFO @ Sat, 11 Dec 2021 07:11:50: 5000000 INFO @ Sat, 11 Dec 2021 07:11:52: 14000000 INFO @ Sat, 11 Dec 2021 07:11:55: 10000000 INFO @ Sat, 11 Dec 2021 07:11:57: 6000000 INFO @ Sat, 11 Dec 2021 07:11:59: 15000000 INFO @ Sat, 11 Dec 2021 07:12:02: 11000000 INFO @ Sat, 11 Dec 2021 07:12:05: 7000000 INFO @ Sat, 11 Dec 2021 07:12:07: 16000000 INFO @ Sat, 11 Dec 2021 07:12:09: 12000000 INFO @ Sat, 11 Dec 2021 07:12:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:12:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:12:11: #1 total tags in treatment: 16642313 INFO @ Sat, 11 Dec 2021 07:12:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:12:11: #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 07:12:12: #1 tags after filtering in treatment: 16642313 INFO @ Sat, 11 Dec 2021 07:12:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:12:12: #1 finished! INFO @ Sat, 11 Dec 2021 07:12:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:12:13: 8000000 INFO @ Sat, 11 Dec 2021 07:12:13: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 07:12:13: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 07:12:13: start model_add_line... INFO @ Sat, 11 Dec 2021 07:12:13: start X-correlation... INFO @ Sat, 11 Dec 2021 07:12:13: end of X-cor INFO @ Sat, 11 Dec 2021 07:12:13: #2 finished! INFO @ Sat, 11 Dec 2021 07:12:13: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 07:12:13: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 11 Dec 2021 07:12:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.05_model.r WARNING @ Sat, 11 Dec 2021 07:12:13: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:12:13: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 11 Dec 2021 07:12:13: #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 07:12:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:12:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:12:16: 13000000 INFO @ Sat, 11 Dec 2021 07:12:20: 9000000 INFO @ Sat, 11 Dec 2021 07:12:24: 14000000 INFO @ Sat, 11 Dec 2021 07:12:28: 10000000 INFO @ Sat, 11 Dec 2021 07:12:31: 15000000 INFO @ Sat, 11 Dec 2021 07:12:36: 11000000 INFO @ Sat, 11 Dec 2021 07:12:38: 16000000 INFO @ Sat, 11 Dec 2021 07:12:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:12:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:12:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:12:43: #1 total tags in treatment: 16642313 INFO @ Sat, 11 Dec 2021 07:12:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:12:43: #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 07:12:43: #1 tags after filtering in treatment: 16642313 INFO @ Sat, 11 Dec 2021 07:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:12:43: #1 finished! INFO @ Sat, 11 Dec 2021 07:12:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:12:44: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 07:12:44: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 07:12:44: start model_add_line... INFO @ Sat, 11 Dec 2021 07:12:44: start X-correlation... INFO @ Sat, 11 Dec 2021 07:12:44: end of X-cor INFO @ Sat, 11 Dec 2021 07:12:44: #2 finished! INFO @ Sat, 11 Dec 2021 07:12:44: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 07:12:44: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 11 Dec 2021 07:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.10_model.r WARNING @ Sat, 11 Dec 2021 07:12:44: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:12:44: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 11 Dec 2021 07:12:44: #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 07:12:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:12:44: 12000000 INFO @ Sat, 11 Dec 2021 07:12:53: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:12:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:12:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:12:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.05_summits.bed INFO @ Sat, 11 Dec 2021 07:12:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2187 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:13:00: 14000000 INFO @ Sat, 11 Dec 2021 07:13:07: 15000000 INFO @ Sat, 11 Dec 2021 07:13:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:13:15: 16000000 INFO @ Sat, 11 Dec 2021 07:13:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:13:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:13:19: #1 total tags in treatment: 16642313 INFO @ Sat, 11 Dec 2021 07:13:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:13:19: #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 07:13:20: #1 tags after filtering in treatment: 16642313 INFO @ Sat, 11 Dec 2021 07:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:13:20: #1 finished! INFO @ Sat, 11 Dec 2021 07:13:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:13:21: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 07:13:21: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 07:13:21: start model_add_line... INFO @ Sat, 11 Dec 2021 07:13:21: start X-correlation... INFO @ Sat, 11 Dec 2021 07:13:21: end of X-cor INFO @ Sat, 11 Dec 2021 07:13:21: #2 finished! INFO @ Sat, 11 Dec 2021 07:13:21: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 07:13:21: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 11 Dec 2021 07:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.20_model.r WARNING @ Sat, 11 Dec 2021 07:13:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:13:21: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 11 Dec 2021 07:13:21: #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 07:13:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:13:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:13:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:13:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.10_summits.bed INFO @ Sat, 11 Dec 2021 07:13:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1540 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:13:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689044/SRX8689044.20_summits.bed INFO @ Sat, 11 Dec 2021 07:14:06: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1069 records, 4 fields): 3 millis CompletedMACS2peakCalling