Job ID = 6626996 SRX = SRX7988219 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:13:57 prefetch.2.10.7: 1) Downloading 'SRR11409517'... 2020-07-14T00:13:57 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:15:01 prefetch.2.10.7 int: connection failed while opening file within cryptographic module - Cannot KNSManagerMakeClientRequest: https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011142/SRR11409517 2020-07-14T00:15:01 prefetch.2.10.7: HTTPS download failed 2020-07-14T00:15:01 prefetch.2.10.7: 1) failed to download SRR11409517 2020-07-14T00:15:11 prefetch.2.10.7: 1) Downloading 'SRR11409517'... 2020-07-14T00:15:11 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:21:03 prefetch.2.10.7: HTTPS download failed 2020-07-14T00:21:03 prefetch.2.10.7: 1) failed to download SRR11409517 2020-07-14T00:21:13 prefetch.2.10.7: 1) Downloading 'SRR11409517'... 2020-07-14T00:21:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:21:13 prefetch.2.10.7: Continue download of 'SRR11409517' from 1271732227 2020-07-14T00:21:36 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:21:36 prefetch.2.10.7: 1) 'SRR11409517' was downloaded successfully 2020-07-14T00:21:36 prefetch.2.10.7: 'SRR11409517' has 0 unresolved dependencies Read 23481704 spots for SRR11409517/SRR11409517.sra Written 23481704 spots for SRR11409517/SRR11409517.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627346 ("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: 00:51:03 23481704 reads; of these: 23481704 (100.00%) were paired; of these: 3103940 (13.22%) aligned concordantly 0 times 14566109 (62.03%) aligned concordantly exactly 1 time 5811655 (24.75%) aligned concordantly >1 times ---- 3103940 pairs aligned concordantly 0 times; of these: 953958 (30.73%) aligned discordantly 1 time ---- 2149982 pairs aligned 0 times concordantly or discordantly; of these: 4299964 mates make up the pairs; of these: 2863660 (66.60%) aligned 0 times 626670 (14.57%) aligned exactly 1 time 809634 (18.83%) aligned >1 times 93.90% overall alignment rate Time searching: 00:51:03 Overall time: 00:51:03 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1512737 / 21241439 = 0.0712 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.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 @ Tue, 14 Jul 2020 10:26:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:26:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:26:24: 1000000 INFO @ Tue, 14 Jul 2020 10:26:30: 2000000 INFO @ Tue, 14 Jul 2020 10:26:36: 3000000 INFO @ Tue, 14 Jul 2020 10:26:41: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:26:47: 5000000 INFO @ Tue, 14 Jul 2020 10:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.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 @ Tue, 14 Jul 2020 10:26:48: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:26:48: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:26:55: 6000000 INFO @ Tue, 14 Jul 2020 10:26:57: 1000000 INFO @ Tue, 14 Jul 2020 10:27:02: 7000000 INFO @ Tue, 14 Jul 2020 10:27:05: 2000000 INFO @ Tue, 14 Jul 2020 10:27:10: 8000000 INFO @ Tue, 14 Jul 2020 10:27:14: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:27:17: 9000000 INFO @ Tue, 14 Jul 2020 10:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.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 @ Tue, 14 Jul 2020 10:27:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:27:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:27:23: 4000000 INFO @ Tue, 14 Jul 2020 10:27:25: 10000000 INFO @ Tue, 14 Jul 2020 10:27:27: 1000000 INFO @ Tue, 14 Jul 2020 10:27:32: 5000000 INFO @ Tue, 14 Jul 2020 10:27:33: 11000000 INFO @ Tue, 14 Jul 2020 10:27:36: 2000000 INFO @ Tue, 14 Jul 2020 10:27:41: 12000000 INFO @ Tue, 14 Jul 2020 10:27:41: 6000000 INFO @ Tue, 14 Jul 2020 10:27:44: 3000000 INFO @ Tue, 14 Jul 2020 10:27:48: 13000000 INFO @ Tue, 14 Jul 2020 10:27:49: 7000000 INFO @ Tue, 14 Jul 2020 10:27:53: 4000000 INFO @ Tue, 14 Jul 2020 10:27:56: 14000000 INFO @ Tue, 14 Jul 2020 10:27:58: 8000000 INFO @ Tue, 14 Jul 2020 10:28:02: 5000000 INFO @ Tue, 14 Jul 2020 10:28:04: 15000000 INFO @ Tue, 14 Jul 2020 10:28:06: 9000000 INFO @ Tue, 14 Jul 2020 10:28:10: 6000000 INFO @ Tue, 14 Jul 2020 10:28:12: 16000000 INFO @ Tue, 14 Jul 2020 10:28:15: 10000000 INFO @ Tue, 14 Jul 2020 10:28:18: 7000000 INFO @ Tue, 14 Jul 2020 10:28:19: 17000000 INFO @ Tue, 14 Jul 2020 10:28:23: 11000000 INFO @ Tue, 14 Jul 2020 10:28:27: 8000000 INFO @ Tue, 14 Jul 2020 10:28:27: 18000000 INFO @ Tue, 14 Jul 2020 10:28:32: 12000000 INFO @ Tue, 14 Jul 2020 10:28:35: 19000000 INFO @ Tue, 14 Jul 2020 10:28:35: 9000000 INFO @ Tue, 14 Jul 2020 10:28:40: 13000000 INFO @ Tue, 14 Jul 2020 10:28:42: 20000000 INFO @ Tue, 14 Jul 2020 10:28:44: 10000000 INFO @ Tue, 14 Jul 2020 10:28:48: 14000000 INFO @ Tue, 14 Jul 2020 10:28:50: 21000000 INFO @ Tue, 14 Jul 2020 10:28:52: 11000000 INFO @ Tue, 14 Jul 2020 10:28:57: 15000000 INFO @ Tue, 14 Jul 2020 10:28:58: 22000000 INFO @ Tue, 14 Jul 2020 10:29:00: 12000000 INFO @ Tue, 14 Jul 2020 10:29:05: 16000000 INFO @ Tue, 14 Jul 2020 10:29:06: 23000000 INFO @ Tue, 14 Jul 2020 10:29:09: 13000000 INFO @ Tue, 14 Jul 2020 10:29:13: 17000000 INFO @ Tue, 14 Jul 2020 10:29:13: 24000000 INFO @ Tue, 14 Jul 2020 10:29:17: 14000000 INFO @ Tue, 14 Jul 2020 10:29:21: 25000000 INFO @ Tue, 14 Jul 2020 10:29:21: 18000000 INFO @ Tue, 14 Jul 2020 10:29:25: 15000000 INFO @ Tue, 14 Jul 2020 10:29:29: 26000000 INFO @ Tue, 14 Jul 2020 10:29:30: 19000000 INFO @ Tue, 14 Jul 2020 10:29:33: 16000000 INFO @ Tue, 14 Jul 2020 10:29:36: 27000000 INFO @ Tue, 14 Jul 2020 10:29:38: 20000000 INFO @ Tue, 14 Jul 2020 10:29:42: 17000000 INFO @ Tue, 14 Jul 2020 10:29:44: 28000000 INFO @ Tue, 14 Jul 2020 10:29:47: 21000000 INFO @ Tue, 14 Jul 2020 10:29:50: 18000000 INFO @ Tue, 14 Jul 2020 10:29:51: 29000000 INFO @ Tue, 14 Jul 2020 10:29:55: 22000000 INFO @ Tue, 14 Jul 2020 10:29:59: 30000000 INFO @ Tue, 14 Jul 2020 10:29:59: 19000000 INFO @ Tue, 14 Jul 2020 10:30:04: 23000000 INFO @ Tue, 14 Jul 2020 10:30:07: 31000000 INFO @ Tue, 14 Jul 2020 10:30:08: 20000000 INFO @ Tue, 14 Jul 2020 10:30:12: 24000000 INFO @ Tue, 14 Jul 2020 10:30:14: 32000000 INFO @ Tue, 14 Jul 2020 10:30:17: 21000000 INFO @ Tue, 14 Jul 2020 10:30:21: 25000000 INFO @ Tue, 14 Jul 2020 10:30:22: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:30:25: 22000000 INFO @ Tue, 14 Jul 2020 10:30:29: 34000000 INFO @ Tue, 14 Jul 2020 10:30:30: 26000000 INFO @ Tue, 14 Jul 2020 10:30:34: 23000000 INFO @ Tue, 14 Jul 2020 10:30:37: 35000000 INFO @ Tue, 14 Jul 2020 10:30:39: 27000000 INFO @ Tue, 14 Jul 2020 10:30:43: 24000000 INFO @ Tue, 14 Jul 2020 10:30:45: 36000000 INFO @ Tue, 14 Jul 2020 10:30:48: 28000000 INFO @ Tue, 14 Jul 2020 10:30:52: 25000000 INFO @ Tue, 14 Jul 2020 10:30:53: 37000000 INFO @ Tue, 14 Jul 2020 10:30:56: 29000000 INFO @ Tue, 14 Jul 2020 10:31:00: 38000000 INFO @ Tue, 14 Jul 2020 10:31:01: 26000000 INFO @ Tue, 14 Jul 2020 10:31:05: 30000000 INFO @ Tue, 14 Jul 2020 10:31:08: 39000000 INFO @ Tue, 14 Jul 2020 10:31:10: 27000000 INFO @ Tue, 14 Jul 2020 10:31:14: 31000000 INFO @ Tue, 14 Jul 2020 10:31:16: 40000000 INFO @ Tue, 14 Jul 2020 10:31:19: 28000000 INFO @ Tue, 14 Jul 2020 10:31:22: 32000000 INFO @ Tue, 14 Jul 2020 10:31:23: 41000000 INFO @ Tue, 14 Jul 2020 10:31:24: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 10:31:24: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 10:31:24: #1 total tags in treatment: 18933085 INFO @ Tue, 14 Jul 2020 10:31:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:31:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:31:24: #1 tags after filtering in treatment: 16834681 INFO @ Tue, 14 Jul 2020 10:31:24: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 10:31:24: #1 finished! INFO @ Tue, 14 Jul 2020 10:31:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:31:25: #2 number of paired peaks: 44 WARNING @ Tue, 14 Jul 2020 10:31:25: Too few paired peaks (44) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Tue, 14 Jul 2020 10:31:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:31:28: 29000000 INFO @ Tue, 14 Jul 2020 10:31:31: 33000000 INFO @ Tue, 14 Jul 2020 10:31:37: 30000000 INFO @ Tue, 14 Jul 2020 10:31:39: 34000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:31:46: 31000000 INFO @ Tue, 14 Jul 2020 10:31:47: 35000000 INFO @ Tue, 14 Jul 2020 10:31:54: 32000000 INFO @ Tue, 14 Jul 2020 10:31:55: 36000000 INFO @ Tue, 14 Jul 2020 10:32:03: 37000000 INFO @ Tue, 14 Jul 2020 10:32:03: 33000000 INFO @ Tue, 14 Jul 2020 10:32:12: 38000000 INFO @ Tue, 14 Jul 2020 10:32:12: 34000000 INFO @ Tue, 14 Jul 2020 10:32:20: 39000000 INFO @ Tue, 14 Jul 2020 10:32:21: 35000000 INFO @ Tue, 14 Jul 2020 10:32:28: 40000000 INFO @ Tue, 14 Jul 2020 10:32:30: 36000000 INFO @ Tue, 14 Jul 2020 10:32:36: 41000000 INFO @ Tue, 14 Jul 2020 10:32:37: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 10:32:37: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 10:32:37: #1 total tags in treatment: 18933085 INFO @ Tue, 14 Jul 2020 10:32:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:32:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:32:37: #1 tags after filtering in treatment: 16834681 INFO @ Tue, 14 Jul 2020 10:32:37: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 10:32:37: #1 finished! INFO @ Tue, 14 Jul 2020 10:32:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:32:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:32:38: #2 number of paired peaks: 44 WARNING @ Tue, 14 Jul 2020 10:32:38: Too few paired peaks (44) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Tue, 14 Jul 2020 10:32:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:32:39: 37000000 INFO @ Tue, 14 Jul 2020 10:32:47: 38000000 INFO @ Tue, 14 Jul 2020 10:32:55: 39000000 INFO @ Tue, 14 Jul 2020 10:33:03: 40000000 INFO @ Tue, 14 Jul 2020 10:33:11: 41000000 INFO @ Tue, 14 Jul 2020 10:33:11: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 10:33:11: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 10:33:11: #1 total tags in treatment: 18933085 INFO @ Tue, 14 Jul 2020 10:33:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:33:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:33:11: #1 tags after filtering in treatment: 16834681 INFO @ Tue, 14 Jul 2020 10:33:11: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 10:33:11: #1 finished! INFO @ Tue, 14 Jul 2020 10:33:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:33:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:33:13: #2 number of paired peaks: 44 WARNING @ Tue, 14 Jul 2020 10:33:13: Too few paired peaks (44) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Tue, 14 Jul 2020 10:33:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX7988219/SRX7988219.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling