Job ID = 14159524 SRX = SRX8845635 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 107854066 spots for SRR12345942/SRR12345942.sra Written 107854066 spots for SRR12345942/SRR12345942.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159781 ("srTce11") 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: 00:14:16 107854066 reads; of these: 107854066 (100.00%) were unpaired; of these: 80395937 (74.54%) aligned 0 times 22592511 (20.95%) aligned exactly 1 time 4865618 (4.51%) aligned >1 times 25.46% overall alignment rate Time searching: 00:14:17 Overall time: 00:14:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4317412 / 27458129 = 0.1572 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 @ Wed, 08 Dec 2021 22:47:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 22:47:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:47:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:47:26: 1000000 INFO @ Wed, 08 Dec 2021 22:47:34: 2000000 INFO @ Wed, 08 Dec 2021 22:47:42: 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 @ Wed, 08 Dec 2021 22:47:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 22:47:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:47:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:47:50: 4000000 INFO @ Wed, 08 Dec 2021 22:47:58: 1000000 INFO @ Wed, 08 Dec 2021 22:47:58: 5000000 INFO @ Wed, 08 Dec 2021 22:48:06: 6000000 INFO @ Wed, 08 Dec 2021 22:48:09: 2000000 BedGraph に変換中... INFO @ Wed, 08 Dec 2021 22:48:14: 7000000 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 @ Wed, 08 Dec 2021 22:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 22:48:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:48:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:48:19: 3000000 INFO @ Wed, 08 Dec 2021 22:48:23: 8000000 INFO @ Wed, 08 Dec 2021 22:48:27: 1000000 INFO @ Wed, 08 Dec 2021 22:48:29: 4000000 INFO @ Wed, 08 Dec 2021 22:48:32: 9000000 INFO @ Wed, 08 Dec 2021 22:48:36: 2000000 INFO @ Wed, 08 Dec 2021 22:48:39: 5000000 INFO @ Wed, 08 Dec 2021 22:48:41: 10000000 INFO @ Wed, 08 Dec 2021 22:48:45: 3000000 INFO @ Wed, 08 Dec 2021 22:48:50: 6000000 INFO @ Wed, 08 Dec 2021 22:48:50: 11000000 INFO @ Wed, 08 Dec 2021 22:48:54: 4000000 INFO @ Wed, 08 Dec 2021 22:48:59: 12000000 INFO @ Wed, 08 Dec 2021 22:49:00: 7000000 INFO @ Wed, 08 Dec 2021 22:49:02: 5000000 INFO @ Wed, 08 Dec 2021 22:49:08: 13000000 INFO @ Wed, 08 Dec 2021 22:49:11: 8000000 INFO @ Wed, 08 Dec 2021 22:49:12: 6000000 INFO @ Wed, 08 Dec 2021 22:49:17: 14000000 INFO @ Wed, 08 Dec 2021 22:49:21: 9000000 INFO @ Wed, 08 Dec 2021 22:49:21: 7000000 INFO @ Wed, 08 Dec 2021 22:49:26: 15000000 INFO @ Wed, 08 Dec 2021 22:49:31: 8000000 INFO @ Wed, 08 Dec 2021 22:49:32: 10000000 INFO @ Wed, 08 Dec 2021 22:49:36: 16000000 INFO @ Wed, 08 Dec 2021 22:49:41: 9000000 INFO @ Wed, 08 Dec 2021 22:49:43: 11000000 INFO @ Wed, 08 Dec 2021 22:49:46: 17000000 INFO @ Wed, 08 Dec 2021 22:49:51: 10000000 INFO @ Wed, 08 Dec 2021 22:49:54: 12000000 INFO @ Wed, 08 Dec 2021 22:49:56: 18000000 INFO @ Wed, 08 Dec 2021 22:50:01: 11000000 INFO @ Wed, 08 Dec 2021 22:50:05: 13000000 INFO @ Wed, 08 Dec 2021 22:50:05: 19000000 INFO @ Wed, 08 Dec 2021 22:50:10: 12000000 INFO @ Wed, 08 Dec 2021 22:50:14: 20000000 INFO @ Wed, 08 Dec 2021 22:50:15: 14000000 INFO @ Wed, 08 Dec 2021 22:50:19: 13000000 INFO @ Wed, 08 Dec 2021 22:50:23: 21000000 INFO @ Wed, 08 Dec 2021 22:50:26: 15000000 INFO @ Wed, 08 Dec 2021 22:50:28: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:50:33: 22000000 INFO @ Wed, 08 Dec 2021 22:50:37: 16000000 INFO @ Wed, 08 Dec 2021 22:50:38: 15000000 INFO @ Wed, 08 Dec 2021 22:50:43: 23000000 INFO @ Wed, 08 Dec 2021 22:50:44: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:50:44: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:50:44: #1 total tags in treatment: 23140717 INFO @ Wed, 08 Dec 2021 22:50:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:50:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:50:44: #1 tags after filtering in treatment: 23140717 INFO @ Wed, 08 Dec 2021 22:50:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:50:44: #1 finished! INFO @ Wed, 08 Dec 2021 22:50:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:50:46: #2 number of paired peaks: 170 WARNING @ Wed, 08 Dec 2021 22:50:46: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Wed, 08 Dec 2021 22:50:46: start model_add_line... INFO @ Wed, 08 Dec 2021 22:50:46: start X-correlation... INFO @ Wed, 08 Dec 2021 22:50:46: end of X-cor INFO @ Wed, 08 Dec 2021 22:50:46: #2 finished! INFO @ Wed, 08 Dec 2021 22:50:46: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:50:46: #2 alternative fragment length(s) may be 1,18,45,577 bps INFO @ Wed, 08 Dec 2021 22:50:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.05_model.r WARNING @ Wed, 08 Dec 2021 22:50:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:50:47: #2 You may need to consider one of the other alternative d(s): 1,18,45,577 WARNING @ Wed, 08 Dec 2021 22:50:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:50:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:50:47: 16000000 INFO @ Wed, 08 Dec 2021 22:50:47: 17000000 INFO @ Wed, 08 Dec 2021 22:50:56: 17000000 INFO @ Wed, 08 Dec 2021 22:50:58: 18000000 INFO @ Wed, 08 Dec 2021 22:51:05: 18000000 INFO @ Wed, 08 Dec 2021 22:51:08: 19000000 INFO @ Wed, 08 Dec 2021 22:51:13: 19000000 INFO @ Wed, 08 Dec 2021 22:51:19: 20000000 INFO @ Wed, 08 Dec 2021 22:51:22: 20000000 INFO @ Wed, 08 Dec 2021 22:51:29: 21000000 INFO @ Wed, 08 Dec 2021 22:51:30: 21000000 INFO @ Wed, 08 Dec 2021 22:51:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:51:40: 22000000 INFO @ Wed, 08 Dec 2021 22:51:40: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:51:49: 23000000 INFO @ Wed, 08 Dec 2021 22:51:50: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:51:50: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:51:50: #1 total tags in treatment: 23140717 INFO @ Wed, 08 Dec 2021 22:51:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:51:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:51:50: #1 tags after filtering in treatment: 23140717 INFO @ Wed, 08 Dec 2021 22:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:51:50: #1 finished! INFO @ Wed, 08 Dec 2021 22:51:50: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:51:50: 23000000 INFO @ Wed, 08 Dec 2021 22:51:52: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:51:52: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:51:52: #1 total tags in treatment: 23140717 INFO @ Wed, 08 Dec 2021 22:51:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:51:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:51:52: #2 number of paired peaks: 170 WARNING @ Wed, 08 Dec 2021 22:51:52: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Wed, 08 Dec 2021 22:51:52: start model_add_line... INFO @ Wed, 08 Dec 2021 22:51:52: #1 tags after filtering in treatment: 23140717 INFO @ Wed, 08 Dec 2021 22:51:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:51:52: #1 finished! INFO @ Wed, 08 Dec 2021 22:51:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:51:52: start X-correlation... INFO @ Wed, 08 Dec 2021 22:51:52: end of X-cor INFO @ Wed, 08 Dec 2021 22:51:52: #2 finished! INFO @ Wed, 08 Dec 2021 22:51:52: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:51:52: #2 alternative fragment length(s) may be 1,18,45,577 bps INFO @ Wed, 08 Dec 2021 22:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.20_model.r WARNING @ Wed, 08 Dec 2021 22:51:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:51:52: #2 You may need to consider one of the other alternative d(s): 1,18,45,577 WARNING @ Wed, 08 Dec 2021 22:51:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:51:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:51:54: #2 number of paired peaks: 170 WARNING @ Wed, 08 Dec 2021 22:51:54: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Wed, 08 Dec 2021 22:51:54: start model_add_line... INFO @ Wed, 08 Dec 2021 22:51:54: start X-correlation... INFO @ Wed, 08 Dec 2021 22:51:54: end of X-cor INFO @ Wed, 08 Dec 2021 22:51:54: #2 finished! INFO @ Wed, 08 Dec 2021 22:51:54: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:51:54: #2 alternative fragment length(s) may be 1,18,45,577 bps INFO @ Wed, 08 Dec 2021 22:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.10_model.r WARNING @ Wed, 08 Dec 2021 22:51:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:51:54: #2 You may need to consider one of the other alternative d(s): 1,18,45,577 WARNING @ Wed, 08 Dec 2021 22:51:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:51:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.05_summits.bed INFO @ Wed, 08 Dec 2021 22:51:57: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:52:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:52:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.20_summits.bed INFO @ Wed, 08 Dec 2021 22:53:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:53:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845635/SRX8845635.10_summits.bed INFO @ Wed, 08 Dec 2021 22:53:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling