Job ID = 14171057 SRX = SRX7320032 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:08 50047200 reads; of these: 50047200 (100.00%) were unpaired; of these: 1804288 (3.61%) aligned 0 times 37775911 (75.48%) aligned exactly 1 time 10467001 (20.91%) aligned >1 times 96.39% overall alignment rate Time searching: 00:12:08 Overall time: 00:12:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 11241754 / 48242912 = 0.2330 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 09:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.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 09:36:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:36:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:36:45: 1000000 INFO @ Sat, 11 Dec 2021 09:36:50: 2000000 INFO @ Sat, 11 Dec 2021 09:36:56: 3000000 INFO @ Sat, 11 Dec 2021 09:37:01: 4000000 INFO @ Sat, 11 Dec 2021 09:37:06: 5000000 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 09:37:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.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 09:37:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:37:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:37:11: 6000000 INFO @ Sat, 11 Dec 2021 09:37:15: 1000000 INFO @ Sat, 11 Dec 2021 09:37:16: 7000000 INFO @ Sat, 11 Dec 2021 09:37:19: 2000000 INFO @ Sat, 11 Dec 2021 09:37:22: 8000000 INFO @ Sat, 11 Dec 2021 09:37:24: 3000000 INFO @ Sat, 11 Dec 2021 09:37:27: 9000000 INFO @ Sat, 11 Dec 2021 09:37:29: 4000000 INFO @ Sat, 11 Dec 2021 09:37:32: 10000000 INFO @ Sat, 11 Dec 2021 09:37:33: 5000000 INFO @ Sat, 11 Dec 2021 09:37:37: 11000000 INFO @ Sat, 11 Dec 2021 09:37:38: 6000000 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 09:37:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.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 09:37:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:37:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:37:42: 12000000 INFO @ Sat, 11 Dec 2021 09:37:43: 7000000 INFO @ Sat, 11 Dec 2021 09:37:46: 1000000 INFO @ Sat, 11 Dec 2021 09:37:48: 13000000 INFO @ Sat, 11 Dec 2021 09:37:48: 8000000 INFO @ Sat, 11 Dec 2021 09:37:51: 2000000 INFO @ Sat, 11 Dec 2021 09:37:52: 9000000 INFO @ Sat, 11 Dec 2021 09:37:53: 14000000 INFO @ Sat, 11 Dec 2021 09:37:56: 3000000 INFO @ Sat, 11 Dec 2021 09:37:57: 10000000 INFO @ Sat, 11 Dec 2021 09:37:58: 15000000 INFO @ Sat, 11 Dec 2021 09:38:01: 4000000 INFO @ Sat, 11 Dec 2021 09:38:02: 11000000 INFO @ Sat, 11 Dec 2021 09:38:03: 16000000 INFO @ Sat, 11 Dec 2021 09:38:07: 5000000 INFO @ Sat, 11 Dec 2021 09:38:07: 12000000 INFO @ Sat, 11 Dec 2021 09:38:09: 17000000 INFO @ Sat, 11 Dec 2021 09:38:11: 13000000 INFO @ Sat, 11 Dec 2021 09:38:12: 6000000 INFO @ Sat, 11 Dec 2021 09:38:14: 18000000 INFO @ Sat, 11 Dec 2021 09:38:16: 14000000 INFO @ Sat, 11 Dec 2021 09:38:17: 7000000 INFO @ Sat, 11 Dec 2021 09:38:19: 19000000 INFO @ Sat, 11 Dec 2021 09:38:21: 15000000 INFO @ Sat, 11 Dec 2021 09:38:22: 8000000 INFO @ Sat, 11 Dec 2021 09:38:25: 20000000 INFO @ Sat, 11 Dec 2021 09:38:26: 16000000 INFO @ Sat, 11 Dec 2021 09:38:28: 9000000 INFO @ Sat, 11 Dec 2021 09:38:30: 21000000 INFO @ Sat, 11 Dec 2021 09:38:30: 17000000 INFO @ Sat, 11 Dec 2021 09:38:33: 10000000 INFO @ Sat, 11 Dec 2021 09:38:35: 18000000 INFO @ Sat, 11 Dec 2021 09:38:35: 22000000 INFO @ Sat, 11 Dec 2021 09:38:38: 11000000 INFO @ Sat, 11 Dec 2021 09:38:40: 19000000 INFO @ Sat, 11 Dec 2021 09:38:40: 23000000 INFO @ Sat, 11 Dec 2021 09:38:44: 12000000 INFO @ Sat, 11 Dec 2021 09:38:45: 20000000 INFO @ Sat, 11 Dec 2021 09:38:46: 24000000 INFO @ Sat, 11 Dec 2021 09:38:49: 13000000 INFO @ Sat, 11 Dec 2021 09:38:49: 21000000 INFO @ Sat, 11 Dec 2021 09:38:51: 25000000 INFO @ Sat, 11 Dec 2021 09:38:54: 22000000 INFO @ Sat, 11 Dec 2021 09:38:54: 14000000 INFO @ Sat, 11 Dec 2021 09:38:57: 26000000 INFO @ Sat, 11 Dec 2021 09:38:59: 23000000 INFO @ Sat, 11 Dec 2021 09:38:59: 15000000 INFO @ Sat, 11 Dec 2021 09:39:02: 27000000 INFO @ Sat, 11 Dec 2021 09:39:03: 24000000 INFO @ Sat, 11 Dec 2021 09:39:05: 16000000 INFO @ Sat, 11 Dec 2021 09:39:08: 28000000 INFO @ Sat, 11 Dec 2021 09:39:08: 25000000 INFO @ Sat, 11 Dec 2021 09:39:10: 17000000 INFO @ Sat, 11 Dec 2021 09:39:13: 26000000 INFO @ Sat, 11 Dec 2021 09:39:13: 29000000 INFO @ Sat, 11 Dec 2021 09:39:15: 18000000 INFO @ Sat, 11 Dec 2021 09:39:18: 27000000 INFO @ Sat, 11 Dec 2021 09:39:19: 30000000 INFO @ Sat, 11 Dec 2021 09:39:20: 19000000 INFO @ Sat, 11 Dec 2021 09:39:23: 28000000 INFO @ Sat, 11 Dec 2021 09:39:24: 31000000 INFO @ Sat, 11 Dec 2021 09:39:26: 20000000 INFO @ Sat, 11 Dec 2021 09:39:27: 29000000 INFO @ Sat, 11 Dec 2021 09:39:29: 32000000 INFO @ Sat, 11 Dec 2021 09:39:31: 21000000 INFO @ Sat, 11 Dec 2021 09:39:32: 30000000 INFO @ Sat, 11 Dec 2021 09:39:35: 33000000 INFO @ Sat, 11 Dec 2021 09:39:36: 22000000 INFO @ Sat, 11 Dec 2021 09:39:37: 31000000 INFO @ Sat, 11 Dec 2021 09:39:40: 34000000 INFO @ Sat, 11 Dec 2021 09:39:41: 23000000 INFO @ Sat, 11 Dec 2021 09:39:42: 32000000 INFO @ Sat, 11 Dec 2021 09:39:45: 35000000 INFO @ Sat, 11 Dec 2021 09:39:47: 33000000 INFO @ Sat, 11 Dec 2021 09:39:47: 24000000 INFO @ Sat, 11 Dec 2021 09:39:50: 36000000 INFO @ Sat, 11 Dec 2021 09:39:51: 34000000 INFO @ Sat, 11 Dec 2021 09:39:52: 25000000 INFO @ Sat, 11 Dec 2021 09:39:56: 37000000 INFO @ Sat, 11 Dec 2021 09:39:56: #1 tag size is determined as 49 bps INFO @ Sat, 11 Dec 2021 09:39:56: #1 tag size = 49 INFO @ Sat, 11 Dec 2021 09:39:56: #1 total tags in treatment: 37001158 INFO @ Sat, 11 Dec 2021 09:39:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:39:56: #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 09:39:56: 35000000 INFO @ Sat, 11 Dec 2021 09:39:57: #1 tags after filtering in treatment: 37001158 INFO @ Sat, 11 Dec 2021 09:39:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:39:57: #1 finished! INFO @ Sat, 11 Dec 2021 09:39:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:39:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:39:57: 26000000 INFO @ Sat, 11 Dec 2021 09:39:59: #2 number of paired peaks: 109 WARNING @ Sat, 11 Dec 2021 09:39:59: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 11 Dec 2021 09:39:59: start model_add_line... INFO @ Sat, 11 Dec 2021 09:39:59: start X-correlation... INFO @ Sat, 11 Dec 2021 09:39:59: end of X-cor INFO @ Sat, 11 Dec 2021 09:39:59: #2 finished! INFO @ Sat, 11 Dec 2021 09:39:59: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 09:39:59: #2 alternative fragment length(s) may be 1,44,433,464,552,587 bps INFO @ Sat, 11 Dec 2021 09:39:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.05_model.r WARNING @ Sat, 11 Dec 2021 09:39:59: #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 09:39:59: #2 You may need to consider one of the other alternative d(s): 1,44,433,464,552,587 WARNING @ Sat, 11 Dec 2021 09:39:59: #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 09:39:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:39:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:40:01: 36000000 INFO @ Sat, 11 Dec 2021 09:40:02: 27000000 INFO @ Sat, 11 Dec 2021 09:40:06: 37000000 INFO @ Sat, 11 Dec 2021 09:40:06: #1 tag size is determined as 49 bps INFO @ Sat, 11 Dec 2021 09:40:06: #1 tag size = 49 INFO @ Sat, 11 Dec 2021 09:40:06: #1 total tags in treatment: 37001158 INFO @ Sat, 11 Dec 2021 09:40:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:40:06: #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 09:40:07: #1 tags after filtering in treatment: 37001158 INFO @ Sat, 11 Dec 2021 09:40:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:40:07: #1 finished! INFO @ Sat, 11 Dec 2021 09:40:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:40:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:40:08: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:40:09: #2 number of paired peaks: 109 WARNING @ Sat, 11 Dec 2021 09:40:09: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 11 Dec 2021 09:40:09: start model_add_line... INFO @ Sat, 11 Dec 2021 09:40:09: start X-correlation... INFO @ Sat, 11 Dec 2021 09:40:09: end of X-cor INFO @ Sat, 11 Dec 2021 09:40:09: #2 finished! INFO @ Sat, 11 Dec 2021 09:40:09: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 09:40:09: #2 alternative fragment length(s) may be 1,44,433,464,552,587 bps INFO @ Sat, 11 Dec 2021 09:40:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.10_model.r WARNING @ Sat, 11 Dec 2021 09:40:09: #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 09:40:09: #2 You may need to consider one of the other alternative d(s): 1,44,433,464,552,587 WARNING @ Sat, 11 Dec 2021 09:40:09: #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 09:40:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:40:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:40:13: 29000000 INFO @ Sat, 11 Dec 2021 09:40:18: 30000000 INFO @ Sat, 11 Dec 2021 09:40:23: 31000000 INFO @ Sat, 11 Dec 2021 09:40:28: 32000000 INFO @ Sat, 11 Dec 2021 09:40:33: 33000000 INFO @ Sat, 11 Dec 2021 09:40:39: 34000000 INFO @ Sat, 11 Dec 2021 09:40:44: 35000000 INFO @ Sat, 11 Dec 2021 09:40:49: 36000000 INFO @ Sat, 11 Dec 2021 09:40:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:40:54: 37000000 INFO @ Sat, 11 Dec 2021 09:40:54: #1 tag size is determined as 49 bps INFO @ Sat, 11 Dec 2021 09:40:54: #1 tag size = 49 INFO @ Sat, 11 Dec 2021 09:40:54: #1 total tags in treatment: 37001158 INFO @ Sat, 11 Dec 2021 09:40:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:40:54: #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 09:40:55: #1 tags after filtering in treatment: 37001158 INFO @ Sat, 11 Dec 2021 09:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:40:55: #1 finished! INFO @ Sat, 11 Dec 2021 09:40:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:40:57: #2 number of paired peaks: 109 WARNING @ Sat, 11 Dec 2021 09:40:57: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 11 Dec 2021 09:40:57: start model_add_line... INFO @ Sat, 11 Dec 2021 09:40:57: start X-correlation... INFO @ Sat, 11 Dec 2021 09:40:57: end of X-cor INFO @ Sat, 11 Dec 2021 09:40:57: #2 finished! INFO @ Sat, 11 Dec 2021 09:40:57: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 09:40:57: #2 alternative fragment length(s) may be 1,44,433,464,552,587 bps INFO @ Sat, 11 Dec 2021 09:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.20_model.r WARNING @ Sat, 11 Dec 2021 09:40:57: #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 09:40:57: #2 You may need to consider one of the other alternative d(s): 1,44,433,464,552,587 WARNING @ Sat, 11 Dec 2021 09:40:57: #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 09:40:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:41:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:41:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:41:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:41:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.05_summits.bed INFO @ Sat, 11 Dec 2021 09:41:12: 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。 INFO @ Sat, 11 Dec 2021 09:41:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.10_summits.bed INFO @ Sat, 11 Dec 2021 09:41:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:41:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:42:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:42:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:42:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7320032/SRX7320032.20_summits.bed INFO @ Sat, 11 Dec 2021 09:42:11: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling