[2024-01-24 11:35:11,881] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg19c896a6-3f25-487a-beec-fb69e0a41543/dqc_reference
[2024-01-24 11:35:13,169] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:13,170] [INFO] Task started: Prodigal
[2024-01-24 11:35:13,170] [INFO] Running command: gunzip -c /var/lib/cwl/stgbec11abf-ff7a-43a3-aae7-ebc5579c16e2/GCF_015627175.1_ASM1562717v1_genomic.fna.gz | prodigal -d GCF_015627175.1_ASM1562717v1_genomic.fna/cds.fna -a GCF_015627175.1_ASM1562717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:18,553] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:18,554] [INFO] Task started: HMMsearch
[2024-01-24 11:35:18,554] [INFO] Running command: hmmsearch --tblout GCF_015627175.1_ASM1562717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19c896a6-3f25-487a-beec-fb69e0a41543/dqc_reference/reference_markers.hmm GCF_015627175.1_ASM1562717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:18,805] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:18,806] [INFO] Found 6/6 markers.
[2024-01-24 11:35:18,837] [INFO] Query marker FASTA was written to GCF_015627175.1_ASM1562717v1_genomic.fna/markers.fasta
[2024-01-24 11:35:18,838] [INFO] Task started: Blastn
[2024-01-24 11:35:18,838] [INFO] Running command: blastn -query GCF_015627175.1_ASM1562717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c896a6-3f25-487a-beec-fb69e0a41543/dqc_reference/reference_markers.fasta -out GCF_015627175.1_ASM1562717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:19,560] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:19,564] [INFO] Selected 22 target genomes.
[2024-01-24 11:35:19,564] [INFO] Target genome list was writen to GCF_015627175.1_ASM1562717v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:19,593] [INFO] Task started: fastANI
[2024-01-24 11:35:19,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgbec11abf-ff7a-43a3-aae7-ebc5579c16e2/GCF_015627175.1_ASM1562717v1_genomic.fna.gz --refList GCF_015627175.1_ASM1562717v1_genomic.fna/target_genomes.txt --output GCF_015627175.1_ASM1562717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:31,696] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:31,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19c896a6-3f25-487a-beec-fb69e0a41543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:31,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19c896a6-3f25-487a-beec-fb69e0a41543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:31,713] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:31,713] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:31,713] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Acinetobacter pollinis	strain=SCC477	GCA_015627175.1	2605270	2605270	type	True	100.0	869	871	95	conclusive
Acinetobacter nectaris	strain=CIP 110549	GCA_000488215.1	1219382	1219382	type	True	84.549	604	871	95	below_threshold
Acinetobacter baretiae	strain=B10A	GCA_015627105.1	2605383	2605383	type	True	79.4626	292	871	95	below_threshold
Acinetobacter rathckeae	strain=EC24	GCA_015627125.1	2605272	2605272	type	True	79.2577	290	871	95	below_threshold
Acinetobacter brisouii	strain=CIP 110357	GCA_000488275.1	396323	396323	type	True	78.6929	210	871	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_000737145.1	470	470	type	True	78.6003	193	871	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	78.5902	190	871	95	below_threshold
Acinetobacter brisouii	strain=DSM 18516	GCA_000931655.1	396323	396323	type	True	78.5712	206	871	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	78.571	189	871	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	78.5169	197	871	95	below_threshold
Acinetobacter oleivorans	strain=KCTC 23045	GCA_000836035.1	1148157	1148157	suspected-type	True	78.4934	191	871	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	78.4774	226	871	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_014116795.1	470	470	type	True	78.4613	195	871	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	78.3996	193	871	95	below_threshold
Acinetobacter bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	78.3755	187	871	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	78.3219	171	871	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	78.3193	197	871	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	78.2799	194	871	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	78.2288	130	871	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	78.2265	177	871	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:31,715] [INFO] DFAST Taxonomy check result was written to GCF_015627175.1_ASM1562717v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:31,716] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:31,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:31,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19c896a6-3f25-487a-beec-fb69e0a41543/dqc_reference/checkm_data
[2024-01-24 11:35:31,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:31,746] [INFO] Task started: CheckM
[2024-01-24 11:35:31,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015627175.1_ASM1562717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015627175.1_ASM1562717v1_genomic.fna/checkm_input GCF_015627175.1_ASM1562717v1_genomic.fna/checkm_result
[2024-01-24 11:35:55,318] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:55,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:55,341] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:55,341] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:55,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015627175.1_ASM1562717v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:55,342] [INFO] Task started: Blastn
[2024-01-24 11:35:55,342] [INFO] Running command: blastn -query GCF_015627175.1_ASM1562717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c896a6-3f25-487a-beec-fb69e0a41543/dqc_reference/reference_markers_gtdb.fasta -out GCF_015627175.1_ASM1562717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:56,482] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:56,491] [INFO] Selected 24 target genomes.
[2024-01-24 11:35:56,491] [INFO] Target genome list was writen to GCF_015627175.1_ASM1562717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:56,513] [INFO] Task started: fastANI
[2024-01-24 11:35:56,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgbec11abf-ff7a-43a3-aae7-ebc5579c16e2/GCF_015627175.1_ASM1562717v1_genomic.fna.gz --refList GCF_015627175.1_ASM1562717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015627175.1_ASM1562717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:12,951] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:12,975] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:12,975] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_015627175.1	s__Acinetobacter pollinis	100.0	869	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.68	99.51	0.94	0.92	4	conclusive
GCF_000488215.1	s__Acinetobacter nectaris	84.549	604	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015627125.1	s__Acinetobacter rathckeae	79.2688	288	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.78	99.78	0.93	0.93	2	-
GCF_900197575.1	s__Acinetobacter apis	79.1094	296	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009372215.1	s__Acinetobacter portensis	78.5381	196	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
GCF_009759685.1	s__Acinetobacter baumannii	78.5314	193	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.86	96.67	0.89	0.80	5417	-
GCF_008993995.1	s__Acinetobacter brisouii_A	78.4782	218	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.99	97.99	0.89	0.89	2	-
GCF_001307195.1	s__Acinetobacter equi	78.4774	226	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	78.4603	192	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369045.1	s__Acinetobacter pittii	78.448	201	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	-
GCF_000368265.1	s__Acinetobacter sp000368265	78.4383	217	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.84	96.49	0.89	0.85	3	-
GCF_001605885.1	s__Acinetobacter lactucae	78.4279	199	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.34	96.55	0.91	0.85	16	-
GCF_000196795.1	s__Acinetobacter oleivorans	78.4168	194	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.22	95.12	0.90	0.85	40	-
GCF_001696605.3	s__Acinetobacter wuhouensis	78.3996	193	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_000368925.1	s__Acinetobacter bereziniae	78.335	189	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.33	97.29	0.90	0.83	53	-
GCF_003261585.1	s__Acinetobacter sp003261585	78.335	215	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902809855.1	s__Acinetobacter sp902809855	78.3241	179	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647675.1	s__Acinetobacter sp001647675	78.2742	169	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016508255.1	s__Acinetobacter calcoaceticus_E	78.2728	202	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707625.1	s__Acinetobacter sp009707625	78.2699	220	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214135.1	s__Acinetobacter sp000214135	78.2419	207	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678755.1	s__Acinetobacter gandensis	78.2265	177	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	-
GCF_900096895.1	s__Acinetobacter kookii	78.1464	141	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.51	0.92	0.92	2	-
GCF_002135345.1	s__Acinetobacter sp002135345	77.9689	186	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:12,977] [INFO] GTDB search result was written to GCF_015627175.1_ASM1562717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:12,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:12,983] [INFO] DFAST_QC result json was written to GCF_015627175.1_ASM1562717v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:12,983] [INFO] DFAST_QC completed!
[2024-01-24 11:36:12,983] [INFO] Total running time: 0h1m1s