Job ID = 14167446 SRX = SRX8574268 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: 00:17:47 62882314 reads; of these: 62882314 (100.00%) were unpaired; of these: 7436367 (11.83%) aligned 0 times 34990454 (55.64%) aligned exactly 1 time 20455493 (32.53%) aligned >1 times 88.17% overall alignment rate Time searching: 00:17:47 Overall time: 00:17:47 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 24 files... [bam_rmdupse_core] 17713551 / 55445947 = 0.3195 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 @ Fri, 10 Dec 2021 12:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.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 @ Fri, 10 Dec 2021 12:47:12: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:47:12: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:47:17: 1000000 INFO @ Fri, 10 Dec 2021 12:47:23: 2000000 INFO @ Fri, 10 Dec 2021 12:47:28: 3000000 INFO @ Fri, 10 Dec 2021 12:47:33: 4000000 INFO @ Fri, 10 Dec 2021 12:47:39: 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 @ Fri, 10 Dec 2021 12:47:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.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 @ Fri, 10 Dec 2021 12:47:42: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:47:42: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:47:44: 6000000 INFO @ Fri, 10 Dec 2021 12:47:47: 1000000 INFO @ Fri, 10 Dec 2021 12:47:49: 7000000 INFO @ Fri, 10 Dec 2021 12:47:51: 2000000 INFO @ Fri, 10 Dec 2021 12:47:55: 8000000 INFO @ Fri, 10 Dec 2021 12:47:56: 3000000 INFO @ Fri, 10 Dec 2021 12:48:00: 9000000 INFO @ Fri, 10 Dec 2021 12:48:01: 4000000 INFO @ Fri, 10 Dec 2021 12:48:05: 5000000 INFO @ Fri, 10 Dec 2021 12:48:06: 10000000 INFO @ Fri, 10 Dec 2021 12:48:10: 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 @ Fri, 10 Dec 2021 12:48:11: 11000000 INFO @ Fri, 10 Dec 2021 12:48:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.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 @ Fri, 10 Dec 2021 12:48:12: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:48:12: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:48:15: 7000000 INFO @ Fri, 10 Dec 2021 12:48:16: 12000000 INFO @ Fri, 10 Dec 2021 12:48:17: 1000000 INFO @ Fri, 10 Dec 2021 12:48:19: 8000000 INFO @ Fri, 10 Dec 2021 12:48:22: 13000000 INFO @ Fri, 10 Dec 2021 12:48:23: 2000000 INFO @ Fri, 10 Dec 2021 12:48:24: 9000000 INFO @ Fri, 10 Dec 2021 12:48:27: 14000000 INFO @ Fri, 10 Dec 2021 12:48:28: 3000000 INFO @ Fri, 10 Dec 2021 12:48:29: 10000000 INFO @ Fri, 10 Dec 2021 12:48:33: 15000000 INFO @ Fri, 10 Dec 2021 12:48:33: 4000000 INFO @ Fri, 10 Dec 2021 12:48:33: 11000000 INFO @ Fri, 10 Dec 2021 12:48:38: 12000000 INFO @ Fri, 10 Dec 2021 12:48:38: 16000000 INFO @ Fri, 10 Dec 2021 12:48:38: 5000000 INFO @ Fri, 10 Dec 2021 12:48:43: 13000000 INFO @ Fri, 10 Dec 2021 12:48:43: 17000000 INFO @ Fri, 10 Dec 2021 12:48:43: 6000000 INFO @ Fri, 10 Dec 2021 12:48:47: 14000000 INFO @ Fri, 10 Dec 2021 12:48:49: 7000000 INFO @ Fri, 10 Dec 2021 12:48:49: 18000000 INFO @ Fri, 10 Dec 2021 12:48:52: 15000000 INFO @ Fri, 10 Dec 2021 12:48:54: 8000000 INFO @ Fri, 10 Dec 2021 12:48:54: 19000000 INFO @ Fri, 10 Dec 2021 12:48:56: 16000000 INFO @ Fri, 10 Dec 2021 12:48:59: 9000000 INFO @ Fri, 10 Dec 2021 12:48:59: 20000000 INFO @ Fri, 10 Dec 2021 12:49:01: 17000000 INFO @ Fri, 10 Dec 2021 12:49:04: 10000000 INFO @ Fri, 10 Dec 2021 12:49:05: 21000000 INFO @ Fri, 10 Dec 2021 12:49:06: 18000000 INFO @ Fri, 10 Dec 2021 12:49:09: 11000000 INFO @ Fri, 10 Dec 2021 12:49:10: 22000000 INFO @ Fri, 10 Dec 2021 12:49:10: 19000000 INFO @ Fri, 10 Dec 2021 12:49:15: 12000000 INFO @ Fri, 10 Dec 2021 12:49:15: 20000000 INFO @ Fri, 10 Dec 2021 12:49:15: 23000000 INFO @ Fri, 10 Dec 2021 12:49:20: 21000000 INFO @ Fri, 10 Dec 2021 12:49:20: 13000000 INFO @ Fri, 10 Dec 2021 12:49:21: 24000000 INFO @ Fri, 10 Dec 2021 12:49:24: 22000000 INFO @ Fri, 10 Dec 2021 12:49:25: 14000000 INFO @ Fri, 10 Dec 2021 12:49:26: 25000000 INFO @ Fri, 10 Dec 2021 12:49:29: 23000000 INFO @ Fri, 10 Dec 2021 12:49:30: 15000000 INFO @ Fri, 10 Dec 2021 12:49:31: 26000000 INFO @ Fri, 10 Dec 2021 12:49:34: 24000000 INFO @ Fri, 10 Dec 2021 12:49:36: 16000000 INFO @ Fri, 10 Dec 2021 12:49:37: 27000000 INFO @ Fri, 10 Dec 2021 12:49:38: 25000000 INFO @ Fri, 10 Dec 2021 12:49:41: 17000000 INFO @ Fri, 10 Dec 2021 12:49:42: 28000000 INFO @ Fri, 10 Dec 2021 12:49:43: 26000000 INFO @ Fri, 10 Dec 2021 12:49:46: 18000000 INFO @ Fri, 10 Dec 2021 12:49:48: 29000000 INFO @ Fri, 10 Dec 2021 12:49:48: 27000000 INFO @ Fri, 10 Dec 2021 12:49:51: 19000000 INFO @ Fri, 10 Dec 2021 12:49:52: 28000000 INFO @ Fri, 10 Dec 2021 12:49:53: 30000000 INFO @ Fri, 10 Dec 2021 12:49:56: 20000000 INFO @ Fri, 10 Dec 2021 12:49:57: 29000000 INFO @ Fri, 10 Dec 2021 12:49:59: 31000000 INFO @ Fri, 10 Dec 2021 12:50:02: 21000000 INFO @ Fri, 10 Dec 2021 12:50:02: 30000000 INFO @ Fri, 10 Dec 2021 12:50:04: 32000000 INFO @ Fri, 10 Dec 2021 12:50:07: 31000000 INFO @ Fri, 10 Dec 2021 12:50:07: 22000000 INFO @ Fri, 10 Dec 2021 12:50:09: 33000000 INFO @ Fri, 10 Dec 2021 12:50:11: 32000000 INFO @ Fri, 10 Dec 2021 12:50:12: 23000000 INFO @ Fri, 10 Dec 2021 12:50:15: 34000000 INFO @ Fri, 10 Dec 2021 12:50:16: 33000000 INFO @ Fri, 10 Dec 2021 12:50:17: 24000000 INFO @ Fri, 10 Dec 2021 12:50:20: 35000000 INFO @ Fri, 10 Dec 2021 12:50:21: 34000000 INFO @ Fri, 10 Dec 2021 12:50:22: 25000000 INFO @ Fri, 10 Dec 2021 12:50:25: 36000000 INFO @ Fri, 10 Dec 2021 12:50:26: 35000000 INFO @ Fri, 10 Dec 2021 12:50:28: 26000000 INFO @ Fri, 10 Dec 2021 12:50:30: 36000000 INFO @ Fri, 10 Dec 2021 12:50:31: 37000000 INFO @ Fri, 10 Dec 2021 12:50:33: 27000000 INFO @ Fri, 10 Dec 2021 12:50:35: 37000000 INFO @ Fri, 10 Dec 2021 12:50:35: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:50:35: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:50:35: #1 total tags in treatment: 37732396 INFO @ Fri, 10 Dec 2021 12:50:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:50:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:50:36: #1 tags after filtering in treatment: 37732396 INFO @ Fri, 10 Dec 2021 12:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:50:36: #1 finished! INFO @ Fri, 10 Dec 2021 12:50:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:50:38: 28000000 INFO @ Fri, 10 Dec 2021 12:50:38: #2 number of paired peaks: 138 WARNING @ Fri, 10 Dec 2021 12:50:38: 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 @ Fri, 10 Dec 2021 12:50:38: start model_add_line... INFO @ Fri, 10 Dec 2021 12:50:38: start X-correlation... INFO @ Fri, 10 Dec 2021 12:50:38: end of X-cor INFO @ Fri, 10 Dec 2021 12:50:38: #2 finished! INFO @ Fri, 10 Dec 2021 12:50:38: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Dec 2021 12:50:38: #2 alternative fragment length(s) may be 1,34,41 bps INFO @ Fri, 10 Dec 2021 12:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.05_model.r WARNING @ Fri, 10 Dec 2021 12:50:38: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:50:38: #2 You may need to consider one of the other alternative d(s): 1,34,41 WARNING @ Fri, 10 Dec 2021 12:50:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:50:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:50:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:50:39: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:50:39: #1 total tags in treatment: 37732396 INFO @ Fri, 10 Dec 2021 12:50:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:50:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:50:40: #1 tags after filtering in treatment: 37732396 INFO @ Fri, 10 Dec 2021 12:50:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:50:40: #1 finished! INFO @ Fri, 10 Dec 2021 12:50:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:50:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:50:42: #2 number of paired peaks: 138 WARNING @ Fri, 10 Dec 2021 12:50:42: 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 @ Fri, 10 Dec 2021 12:50:42: start model_add_line... INFO @ Fri, 10 Dec 2021 12:50:42: start X-correlation... INFO @ Fri, 10 Dec 2021 12:50:42: end of X-cor INFO @ Fri, 10 Dec 2021 12:50:42: #2 finished! INFO @ Fri, 10 Dec 2021 12:50:42: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Dec 2021 12:50:42: #2 alternative fragment length(s) may be 1,34,41 bps INFO @ Fri, 10 Dec 2021 12:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.10_model.r WARNING @ Fri, 10 Dec 2021 12:50:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:50:42: #2 You may need to consider one of the other alternative d(s): 1,34,41 WARNING @ Fri, 10 Dec 2021 12:50:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:50:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:50:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:50:43: 29000000 INFO @ Fri, 10 Dec 2021 12:50:48: 30000000 INFO @ Fri, 10 Dec 2021 12:50:54: 31000000 INFO @ Fri, 10 Dec 2021 12:50:59: 32000000 INFO @ Fri, 10 Dec 2021 12:51:04: 33000000 INFO @ Fri, 10 Dec 2021 12:51:09: 34000000 INFO @ Fri, 10 Dec 2021 12:51:14: 35000000 INFO @ Fri, 10 Dec 2021 12:51:19: 36000000 INFO @ Fri, 10 Dec 2021 12:51:25: 37000000 INFO @ Fri, 10 Dec 2021 12:51:29: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:51:29: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:51:29: #1 total tags in treatment: 37732396 INFO @ Fri, 10 Dec 2021 12:51:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:51:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:51:30: #1 tags after filtering in treatment: 37732396 INFO @ Fri, 10 Dec 2021 12:51:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:51:30: #1 finished! INFO @ Fri, 10 Dec 2021 12:51:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:51:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:51:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:51:32: #2 number of paired peaks: 138 WARNING @ Fri, 10 Dec 2021 12:51:32: 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 @ Fri, 10 Dec 2021 12:51:32: start model_add_line... INFO @ Fri, 10 Dec 2021 12:51:32: start X-correlation... INFO @ Fri, 10 Dec 2021 12:51:32: end of X-cor INFO @ Fri, 10 Dec 2021 12:51:32: #2 finished! INFO @ Fri, 10 Dec 2021 12:51:32: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Dec 2021 12:51:32: #2 alternative fragment length(s) may be 1,34,41 bps INFO @ Fri, 10 Dec 2021 12:51:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.20_model.r WARNING @ Fri, 10 Dec 2021 12:51:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:51:32: #2 You may need to consider one of the other alternative d(s): 1,34,41 WARNING @ Fri, 10 Dec 2021 12:51:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:51:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:51:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:51:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.05_summits.bed INFO @ Fri, 10 Dec 2021 12:51:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.10_summits.bed INFO @ Fri, 10 Dec 2021 12:51:57: 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 @ Fri, 10 Dec 2021 12:52:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:52:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:52:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:52:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574268/SRX8574268.20_summits.bed INFO @ Fri, 10 Dec 2021 12:52:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling