[2023-06-29 04:25:02,729] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:25:02,732] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:25:02,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg938b7364-ec6f-40df-85c4-66f5e443433a/dqc_reference
[2023-06-29 04:25:05,414] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:25:05,416] [INFO] Task started: Prodigal
[2023-06-29 04:25:05,416] [INFO] Running command: gunzip -c /var/lib/cwl/stgb535b57c-c94b-44cb-8ecd-a8e74daf56ad/GCA_027310565.1_ASM2731056v1_genomic.fna.gz | prodigal -d GCA_027310565.1_ASM2731056v1_genomic.fna/cds.fna -a GCA_027310565.1_ASM2731056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:25:19,599] [INFO] Task succeeded: Prodigal
[2023-06-29 04:25:19,599] [INFO] Task started: HMMsearch
[2023-06-29 04:25:19,599] [INFO] Running command: hmmsearch --tblout GCA_027310565.1_ASM2731056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg938b7364-ec6f-40df-85c4-66f5e443433a/dqc_reference/reference_markers.hmm GCA_027310565.1_ASM2731056v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:25:19,838] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:25:19,840] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb535b57c-c94b-44cb-8ecd-a8e74daf56ad/GCA_027310565.1_ASM2731056v1_genomic.fna.gz]
[2023-06-29 04:25:19,868] [INFO] Query marker FASTA was written to GCA_027310565.1_ASM2731056v1_genomic.fna/markers.fasta
[2023-06-29 04:25:19,868] [INFO] Task started: Blastn
[2023-06-29 04:25:19,869] [INFO] Running command: blastn -query GCA_027310565.1_ASM2731056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg938b7364-ec6f-40df-85c4-66f5e443433a/dqc_reference/reference_markers.fasta -out GCA_027310565.1_ASM2731056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:25:20,539] [INFO] Task succeeded: Blastn
[2023-06-29 04:25:20,544] [INFO] Selected 21 target genomes.
[2023-06-29 04:25:20,545] [INFO] Target genome list was writen to GCA_027310565.1_ASM2731056v1_genomic.fna/target_genomes.txt
[2023-06-29 04:25:20,547] [INFO] Task started: fastANI
[2023-06-29 04:25:20,547] [INFO] Running command: fastANI --query /var/lib/cwl/stgb535b57c-c94b-44cb-8ecd-a8e74daf56ad/GCA_027310565.1_ASM2731056v1_genomic.fna.gz --refList GCA_027310565.1_ASM2731056v1_genomic.fna/target_genomes.txt --output GCA_027310565.1_ASM2731056v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:25:37,656] [INFO] Task succeeded: fastANI
[2023-06-29 04:25:37,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg938b7364-ec6f-40df-85c4-66f5e443433a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:25:37,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg938b7364-ec6f-40df-85c4-66f5e443433a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:25:37,678] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:25:37,678] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:25:37,678] [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
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.1268	262	911	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.1229	332	911	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	75.0362	349	911	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	74.9738	202	911	95	below_threshold
Lysobacter terrigena	strain=17J7-1	GCA_004361065.1	2488749	2488749	type	True	74.9396	89	911	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	74.934	151	911	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	74.9265	181	911	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	74.9236	86	911	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	74.9228	261	911	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	74.9059	213	911	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	74.9	116	911	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	74.8973	104	911	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	74.8776	114	911	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	74.8739	189	911	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	74.8654	234	911	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	74.8441	216	911	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	74.84	283	911	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	74.8366	208	911	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	74.8344	248	911	95	below_threshold
Halobaculum salinum	strain=NJ-3-1	GCA_013402875.1	2743089	2743089	type	True	74.7168	131	911	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:25:37,680] [INFO] DFAST Taxonomy check result was written to GCA_027310565.1_ASM2731056v1_genomic.fna/tc_result.tsv
[2023-06-29 04:25:37,681] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:25:37,681] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:25:37,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg938b7364-ec6f-40df-85c4-66f5e443433a/dqc_reference/checkm_data
[2023-06-29 04:25:37,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:25:37,718] [INFO] Task started: CheckM
[2023-06-29 04:25:37,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310565.1_ASM2731056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310565.1_ASM2731056v1_genomic.fna/checkm_input GCA_027310565.1_ASM2731056v1_genomic.fna/checkm_result
[2023-06-29 04:26:10,724] [INFO] Task succeeded: CheckM
[2023-06-29 04:26:10,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:26:10,748] [INFO] ===== Completeness check finished =====
[2023-06-29 04:26:10,748] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:26:10,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310565.1_ASM2731056v1_genomic.fna/markers.fasta)
[2023-06-29 04:26:10,749] [INFO] Task started: Blastn
[2023-06-29 04:26:10,749] [INFO] Running command: blastn -query GCA_027310565.1_ASM2731056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg938b7364-ec6f-40df-85c4-66f5e443433a/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310565.1_ASM2731056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:26:11,783] [INFO] Task succeeded: Blastn
[2023-06-29 04:26:11,799] [INFO] Selected 10 target genomes.
[2023-06-29 04:26:11,799] [INFO] Target genome list was writen to GCA_027310565.1_ASM2731056v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:26:11,841] [INFO] Task started: fastANI
[2023-06-29 04:26:11,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgb535b57c-c94b-44cb-8ecd-a8e74daf56ad/GCA_027310565.1_ASM2731056v1_genomic.fna.gz --refList GCA_027310565.1_ASM2731056v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310565.1_ASM2731056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:26:17,705] [INFO] Task succeeded: fastANI
[2023-06-29 04:26:17,715] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:26:17,716] [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
GCA_005887995.1	s__CF-39 sp005887995	80.3647	473	911	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__CF-39	95.0	99.25	99.03	0.88	0.87	6	-
GCA_005882255.1	s__CF-39 sp005882255	79.4743	396	911	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__CF-39	95.0	98.81	98.81	0.77	0.77	2	-
GCA_005889405.1	s__CF-39 sp005889405	79.2906	452	911	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__CF-39	95.0	99.10	99.10	0.93	0.93	2	-
GCA_005883625.1	s__3-1-20CM-2-70-9 sp001919195	79.0886	424	911	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__3-1-20CM-2-70-9	95.0	98.45	97.34	0.95	0.95	6	-
GCA_005889275.1	s__3-1-20CM-2-70-9 sp005889275	78.8348	379	911	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__3-1-20CM-2-70-9	95.0	98.44	98.44	0.90	0.90	2	-
GCA_001795345.1	s__GWC2-70-10 sp001795345	78.7303	295	911	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__GWC2-70-10	95.0	98.93	98.93	0.81	0.81	2	-
GCA_005889445.1	s__3-1-20CM-2-70-9 sp005889445	78.4994	274	911	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__3-1-20CM-2-70-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005880575.1	s__3-1-20CM-2-70-9 sp005880575	78.2127	316	911	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__3-1-20CM-2-70-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881885.1	s__3-1-20CM-2-70-9 sp005881885	78.1926	342	911	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__P2-11E;f__P2-11E;g__3-1-20CM-2-70-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003541285.1	s__UBA9676 sp003541285	74.9133	57	911	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__UBA9676	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:26:17,718] [INFO] GTDB search result was written to GCA_027310565.1_ASM2731056v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:26:17,718] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:26:17,723] [INFO] DFAST_QC result json was written to GCA_027310565.1_ASM2731056v1_genomic.fna/dqc_result.json
[2023-06-29 04:26:17,723] [INFO] DFAST_QC completed!
[2023-06-29 04:26:17,723] [INFO] Total running time: 0h1m15s