Job ID = 14170577 SRX = SRX9720895 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31838049 spots for SRR13291885/SRR13291885.sra Written 31838049 spots for SRR13291885/SRR13291885.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171010 ("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: 00:11:24 31838049 reads; of these: 31838049 (100.00%) were unpaired; of these: 1065904 (3.35%) aligned 0 times 20547436 (64.54%) aligned exactly 1 time 10224709 (32.11%) aligned >1 times 96.65% overall alignment rate Time searching: 00:11:24 Overall time: 00:11:24 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] 7166368 / 30772145 = 0.2329 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 07:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.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 07:37:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:37:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:37:13: 1000000 INFO @ Sat, 11 Dec 2021 07:37:18: 2000000 INFO @ Sat, 11 Dec 2021 07:37:23: 3000000 INFO @ Sat, 11 Dec 2021 07:37:27: 4000000 INFO @ Sat, 11 Dec 2021 07:37:32: 5000000 INFO @ Sat, 11 Dec 2021 07:37:37: 6000000 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 07:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.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 07:37:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:37:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:37:41: 7000000 INFO @ Sat, 11 Dec 2021 07:37:45: 1000000 INFO @ Sat, 11 Dec 2021 07:37:46: 8000000 INFO @ Sat, 11 Dec 2021 07:37:51: 2000000 INFO @ Sat, 11 Dec 2021 07:37:51: 9000000 INFO @ Sat, 11 Dec 2021 07:37:56: 10000000 INFO @ Sat, 11 Dec 2021 07:37:56: 3000000 INFO @ Sat, 11 Dec 2021 07:38:01: 11000000 INFO @ Sat, 11 Dec 2021 07:38:02: 4000000 INFO @ Sat, 11 Dec 2021 07:38:06: 12000000 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 07:38:08: 5000000 INFO @ Sat, 11 Dec 2021 07:38:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.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 07:38:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:38:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:38:11: 13000000 INFO @ Sat, 11 Dec 2021 07:38:14: 6000000 INFO @ Sat, 11 Dec 2021 07:38:16: 14000000 INFO @ Sat, 11 Dec 2021 07:38:17: 1000000 INFO @ Sat, 11 Dec 2021 07:38:20: 7000000 INFO @ Sat, 11 Dec 2021 07:38:21: 15000000 INFO @ Sat, 11 Dec 2021 07:38:23: 2000000 INFO @ Sat, 11 Dec 2021 07:38:25: 8000000 INFO @ Sat, 11 Dec 2021 07:38:26: 16000000 INFO @ Sat, 11 Dec 2021 07:38:29: 3000000 INFO @ Sat, 11 Dec 2021 07:38:31: 17000000 INFO @ Sat, 11 Dec 2021 07:38:31: 9000000 INFO @ Sat, 11 Dec 2021 07:38:35: 4000000 INFO @ Sat, 11 Dec 2021 07:38:36: 18000000 INFO @ Sat, 11 Dec 2021 07:38:37: 10000000 INFO @ Sat, 11 Dec 2021 07:38:41: 5000000 INFO @ Sat, 11 Dec 2021 07:38:41: 19000000 INFO @ Sat, 11 Dec 2021 07:38:43: 11000000 INFO @ Sat, 11 Dec 2021 07:38:46: 20000000 INFO @ Sat, 11 Dec 2021 07:38:47: 6000000 INFO @ Sat, 11 Dec 2021 07:38:49: 12000000 INFO @ Sat, 11 Dec 2021 07:38:51: 21000000 INFO @ Sat, 11 Dec 2021 07:38:53: 7000000 INFO @ Sat, 11 Dec 2021 07:38:55: 13000000 INFO @ Sat, 11 Dec 2021 07:38:56: 22000000 INFO @ Sat, 11 Dec 2021 07:38:59: 8000000 INFO @ Sat, 11 Dec 2021 07:39:00: 14000000 INFO @ Sat, 11 Dec 2021 07:39:01: 23000000 INFO @ Sat, 11 Dec 2021 07:39:04: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:39:04: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:39:04: #1 total tags in treatment: 23605777 INFO @ Sat, 11 Dec 2021 07:39:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:39:04: #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 07:39:05: 9000000 INFO @ Sat, 11 Dec 2021 07:39:05: #1 tags after filtering in treatment: 23605777 INFO @ Sat, 11 Dec 2021 07:39:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:39:05: #1 finished! INFO @ Sat, 11 Dec 2021 07:39:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:39:06: 15000000 INFO @ Sat, 11 Dec 2021 07:39:06: #2 number of paired peaks: 468 WARNING @ Sat, 11 Dec 2021 07:39:06: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sat, 11 Dec 2021 07:39:06: start model_add_line... INFO @ Sat, 11 Dec 2021 07:39:07: start X-correlation... INFO @ Sat, 11 Dec 2021 07:39:07: end of X-cor INFO @ Sat, 11 Dec 2021 07:39:07: #2 finished! INFO @ Sat, 11 Dec 2021 07:39:07: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:39:07: #2 alternative fragment length(s) may be 2,48,505 bps INFO @ Sat, 11 Dec 2021 07:39:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.05_model.r WARNING @ Sat, 11 Dec 2021 07:39:07: #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 07:39:07: #2 You may need to consider one of the other alternative d(s): 2,48,505 WARNING @ Sat, 11 Dec 2021 07:39:07: #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 07:39:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:39:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:39:11: 10000000 INFO @ Sat, 11 Dec 2021 07:39:12: 16000000 INFO @ Sat, 11 Dec 2021 07:39:16: 11000000 INFO @ Sat, 11 Dec 2021 07:39:17: 17000000 INFO @ Sat, 11 Dec 2021 07:39:22: 12000000 INFO @ Sat, 11 Dec 2021 07:39:23: 18000000 INFO @ Sat, 11 Dec 2021 07:39:28: 13000000 INFO @ Sat, 11 Dec 2021 07:39:29: 19000000 INFO @ Sat, 11 Dec 2021 07:39:34: 14000000 INFO @ Sat, 11 Dec 2021 07:39:35: 20000000 INFO @ Sat, 11 Dec 2021 07:39:40: 15000000 INFO @ Sat, 11 Dec 2021 07:39:41: 21000000 INFO @ Sat, 11 Dec 2021 07:39:46: 16000000 INFO @ Sat, 11 Dec 2021 07:39:47: 22000000 INFO @ Sat, 11 Dec 2021 07:39:47: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:39:51: 17000000 INFO @ Sat, 11 Dec 2021 07:39:52: 23000000 INFO @ Sat, 11 Dec 2021 07:39:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:39:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:39:56: #1 total tags in treatment: 23605777 INFO @ Sat, 11 Dec 2021 07:39:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:39:56: #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 07:39:56: #1 tags after filtering in treatment: 23605777 INFO @ Sat, 11 Dec 2021 07:39:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:39:56: #1 finished! INFO @ Sat, 11 Dec 2021 07:39:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:39:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:39:57: 18000000 INFO @ Sat, 11 Dec 2021 07:39:58: #2 number of paired peaks: 468 WARNING @ Sat, 11 Dec 2021 07:39:58: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sat, 11 Dec 2021 07:39:58: start model_add_line... INFO @ Sat, 11 Dec 2021 07:39:58: start X-correlation... INFO @ Sat, 11 Dec 2021 07:39:58: end of X-cor INFO @ Sat, 11 Dec 2021 07:39:58: #2 finished! INFO @ Sat, 11 Dec 2021 07:39:58: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:39:58: #2 alternative fragment length(s) may be 2,48,505 bps INFO @ Sat, 11 Dec 2021 07:39:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.10_model.r WARNING @ Sat, 11 Dec 2021 07:39:58: #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 07:39:58: #2 You may need to consider one of the other alternative d(s): 2,48,505 WARNING @ Sat, 11 Dec 2021 07:39:58: #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 07:39:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:39:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:40:03: 19000000 INFO @ Sat, 11 Dec 2021 07:40:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:40:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:40:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.05_summits.bed INFO @ Sat, 11 Dec 2021 07:40:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3797 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:40:08: 20000000 INFO @ Sat, 11 Dec 2021 07:40:14: 21000000 INFO @ Sat, 11 Dec 2021 07:40:19: 22000000 INFO @ Sat, 11 Dec 2021 07:40:25: 23000000 INFO @ Sat, 11 Dec 2021 07:40:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:40:28: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:40:28: #1 total tags in treatment: 23605777 INFO @ Sat, 11 Dec 2021 07:40:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:40:28: #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 07:40:28: #1 tags after filtering in treatment: 23605777 INFO @ Sat, 11 Dec 2021 07:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:40:28: #1 finished! INFO @ Sat, 11 Dec 2021 07:40:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:40:30: #2 number of paired peaks: 468 WARNING @ Sat, 11 Dec 2021 07:40:30: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sat, 11 Dec 2021 07:40:30: start model_add_line... INFO @ Sat, 11 Dec 2021 07:40:30: start X-correlation... INFO @ Sat, 11 Dec 2021 07:40:30: end of X-cor INFO @ Sat, 11 Dec 2021 07:40:30: #2 finished! INFO @ Sat, 11 Dec 2021 07:40:30: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:40:30: #2 alternative fragment length(s) may be 2,48,505 bps INFO @ Sat, 11 Dec 2021 07:40:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.20_model.r WARNING @ Sat, 11 Dec 2021 07:40:30: #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 07:40:30: #2 You may need to consider one of the other alternative d(s): 2,48,505 WARNING @ Sat, 11 Dec 2021 07:40:30: #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 07:40:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:40:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:40:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.10_summits.bed INFO @ Sat, 11 Dec 2021 07:40:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2666 records, 4 fields): 86 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:41:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:41:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:41:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:41:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720895/SRX9720895.20_summits.bed INFO @ Sat, 11 Dec 2021 07:41:30: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1552 records, 4 fields): 3 millis CompletedMACS2peakCalling