Job ID = 14170338 SRX = SRX8689108 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15640097 spots for SRR12174341/SRR12174341.sra Written 15640097 spots for SRR12174341/SRR12174341.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170762 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:08:02 15640097 reads; of these: 15640097 (100.00%) were unpaired; of these: 373325 (2.39%) aligned 0 times 10304271 (65.88%) aligned exactly 1 time 4962501 (31.73%) aligned >1 times 97.61% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 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] 1518527 / 15266772 = 0.0995 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 06:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.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 06:34:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:34:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:35:05: 1000000 INFO @ Sat, 11 Dec 2021 06:35:12: 2000000 INFO @ Sat, 11 Dec 2021 06:35:20: 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 06:35:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.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 06:35:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:35:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:35:28: 4000000 INFO @ Sat, 11 Dec 2021 06:35:35: 1000000 INFO @ Sat, 11 Dec 2021 06:35:36: 5000000 INFO @ Sat, 11 Dec 2021 06:35:42: 2000000 INFO @ Sat, 11 Dec 2021 06:35:44: 6000000 INFO @ Sat, 11 Dec 2021 06:35:49: 3000000 INFO @ Sat, 11 Dec 2021 06:35:52: 7000000 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 06:35:56: 4000000 INFO @ Sat, 11 Dec 2021 06:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.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 06:35:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:35:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:35:59: 8000000 INFO @ Sat, 11 Dec 2021 06:36:04: 5000000 INFO @ Sat, 11 Dec 2021 06:36:06: 1000000 INFO @ Sat, 11 Dec 2021 06:36:07: 9000000 INFO @ Sat, 11 Dec 2021 06:36:11: 6000000 INFO @ Sat, 11 Dec 2021 06:36:15: 10000000 INFO @ Sat, 11 Dec 2021 06:36:15: 2000000 INFO @ Sat, 11 Dec 2021 06:36:18: 7000000 INFO @ Sat, 11 Dec 2021 06:36:23: 11000000 INFO @ Sat, 11 Dec 2021 06:36:24: 3000000 INFO @ Sat, 11 Dec 2021 06:36:25: 8000000 INFO @ Sat, 11 Dec 2021 06:36:31: 12000000 INFO @ Sat, 11 Dec 2021 06:36:33: 9000000 INFO @ Sat, 11 Dec 2021 06:36:33: 4000000 INFO @ Sat, 11 Dec 2021 06:36:39: 13000000 INFO @ Sat, 11 Dec 2021 06:36:40: 10000000 INFO @ Sat, 11 Dec 2021 06:36:42: 5000000 INFO @ Sat, 11 Dec 2021 06:36:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:36:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:36:44: #1 total tags in treatment: 13748245 INFO @ Sat, 11 Dec 2021 06:36:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:36:44: #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 06:36:45: #1 tags after filtering in treatment: 13748245 INFO @ Sat, 11 Dec 2021 06:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:36:45: #1 finished! INFO @ Sat, 11 Dec 2021 06:36:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:36:46: #2 number of paired peaks: 325 WARNING @ Sat, 11 Dec 2021 06:36:46: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Sat, 11 Dec 2021 06:36:46: start model_add_line... INFO @ Sat, 11 Dec 2021 06:36:46: start X-correlation... INFO @ Sat, 11 Dec 2021 06:36:46: end of X-cor INFO @ Sat, 11 Dec 2021 06:36:46: #2 finished! INFO @ Sat, 11 Dec 2021 06:36:46: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 06:36:46: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 11 Dec 2021 06:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.05_model.r WARNING @ Sat, 11 Dec 2021 06:36:46: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:36:46: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 11 Dec 2021 06:36:46: #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 06:36:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:36:48: 11000000 INFO @ Sat, 11 Dec 2021 06:36:51: 6000000 INFO @ Sat, 11 Dec 2021 06:36:55: 12000000 INFO @ Sat, 11 Dec 2021 06:37:00: 7000000 INFO @ Sat, 11 Dec 2021 06:37:02: 13000000 INFO @ Sat, 11 Dec 2021 06:37:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:37:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:37:08: #1 total tags in treatment: 13748245 INFO @ Sat, 11 Dec 2021 06:37:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:37:08: #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 06:37:08: #1 tags after filtering in treatment: 13748245 INFO @ Sat, 11 Dec 2021 06:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:37:08: #1 finished! INFO @ Sat, 11 Dec 2021 06:37:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:37:09: 8000000 INFO @ Sat, 11 Dec 2021 06:37:09: #2 number of paired peaks: 325 WARNING @ Sat, 11 Dec 2021 06:37:09: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Sat, 11 Dec 2021 06:37:09: start model_add_line... INFO @ Sat, 11 Dec 2021 06:37:09: start X-correlation... INFO @ Sat, 11 Dec 2021 06:37:09: end of X-cor INFO @ Sat, 11 Dec 2021 06:37:09: #2 finished! INFO @ Sat, 11 Dec 2021 06:37:09: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 06:37:09: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 11 Dec 2021 06:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.10_model.r WARNING @ Sat, 11 Dec 2021 06:37:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:37:09: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 11 Dec 2021 06:37:09: #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 06:37:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:37:18: 9000000 INFO @ Sat, 11 Dec 2021 06:37:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:37:27: 10000000 INFO @ Sat, 11 Dec 2021 06:37:36: 11000000 INFO @ Sat, 11 Dec 2021 06:37:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:37:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:37:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.05_summits.bed INFO @ Sat, 11 Dec 2021 06:37:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1816 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:37:44: 12000000 INFO @ Sat, 11 Dec 2021 06:37:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:37:53: 13000000 INFO @ Sat, 11 Dec 2021 06:38:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:38:00: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:38:00: #1 total tags in treatment: 13748245 INFO @ Sat, 11 Dec 2021 06:38:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:38:00: #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 06:38:00: #1 tags after filtering in treatment: 13748245 INFO @ Sat, 11 Dec 2021 06:38:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:38:00: #1 finished! INFO @ Sat, 11 Dec 2021 06:38:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:38:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:38:01: #2 number of paired peaks: 325 WARNING @ Sat, 11 Dec 2021 06:38:01: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Sat, 11 Dec 2021 06:38:01: start model_add_line... INFO @ Sat, 11 Dec 2021 06:38:01: start X-correlation... INFO @ Sat, 11 Dec 2021 06:38:01: end of X-cor INFO @ Sat, 11 Dec 2021 06:38:01: #2 finished! INFO @ Sat, 11 Dec 2021 06:38:01: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 06:38:01: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 11 Dec 2021 06:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.20_model.r WARNING @ Sat, 11 Dec 2021 06:38:01: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:38:01: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 11 Dec 2021 06:38:01: #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 06:38:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:38:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:38:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:38:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.10_summits.bed INFO @ Sat, 11 Dec 2021 06:38:04: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1469 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:38:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:38:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:38:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:38:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689108/SRX8689108.20_summits.bed INFO @ Sat, 11 Dec 2021 06:38:56: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1145 records, 4 fields): 4 millis CompletedMACS2peakCalling