[2024-01-25 19:03:50,625] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:50,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:50,626] [INFO] DQC Reference Directory: /var/lib/cwl/stgca73edcd-6bf3-4893-a0cb-1fe081967f9d/dqc_reference
[2024-01-25 19:03:51,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:51,757] [INFO] Task started: Prodigal
[2024-01-25 19:03:51,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fe6901d-4596-409d-bf7b-23e7b929a655/GCF_009724245.1_ASM972424v1_genomic.fna.gz | prodigal -d GCF_009724245.1_ASM972424v1_genomic.fna/cds.fna -a GCF_009724245.1_ASM972424v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:13,119] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:13,120] [INFO] Task started: HMMsearch
[2024-01-25 19:04:13,120] [INFO] Running command: hmmsearch --tblout GCF_009724245.1_ASM972424v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca73edcd-6bf3-4893-a0cb-1fe081967f9d/dqc_reference/reference_markers.hmm GCF_009724245.1_ASM972424v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:13,441] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:13,442] [INFO] Found 6/6 markers.
[2024-01-25 19:04:13,509] [INFO] Query marker FASTA was written to GCF_009724245.1_ASM972424v1_genomic.fna/markers.fasta
[2024-01-25 19:04:13,509] [INFO] Task started: Blastn
[2024-01-25 19:04:13,509] [INFO] Running command: blastn -query GCF_009724245.1_ASM972424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca73edcd-6bf3-4893-a0cb-1fe081967f9d/dqc_reference/reference_markers.fasta -out GCF_009724245.1_ASM972424v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:14,301] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:14,304] [INFO] Selected 31 target genomes.
[2024-01-25 19:04:14,304] [INFO] Target genome list was writen to GCF_009724245.1_ASM972424v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:14,327] [INFO] Task started: fastANI
[2024-01-25 19:04:14,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fe6901d-4596-409d-bf7b-23e7b929a655/GCF_009724245.1_ASM972424v1_genomic.fna.gz --refList GCF_009724245.1_ASM972424v1_genomic.fna/target_genomes.txt --output GCF_009724245.1_ASM972424v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:55,008] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:55,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca73edcd-6bf3-4893-a0cb-1fe081967f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:55,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca73edcd-6bf3-4893-a0cb-1fe081967f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:55,026] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:55,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:55,026] [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
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	100.0	2146	2150	95	conclusive
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	88.0733	1404	2150	95	below_threshold
Pseudomonas yamanorum	strain=LMG 27247	GCA_900105735.1	515393	515393	suspected-type	True	87.5119	1641	2150	95	below_threshold
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	86.5024	1470	2150	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	86.4996	1470	2150	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	86.435	1449	2150	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	86.3193	1441	2150	95	below_threshold
Pseudomonas proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	86.2886	1427	2150	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	86.1906	1478	2150	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	86.1215	1491	2150	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_003700725.1	298	298	suspected-type	True	86.0669	1376	2150	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	85.959	1493	2150	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	85.9404	1533	2150	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	85.917	1494	2150	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	85.8888	1547	2150	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	85.8871	1479	2150	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_900111895.1	321846	321846	type	True	85.8538	1470	2150	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_001730615.1	321846	321846	type	True	85.8004	1474	2150	95	below_threshold
Pseudomonas pisciculturae	strain=P115	GCA_015461805.1	2730413	2730413	type	True	85.6509	1373	2150	95	below_threshold
Pseudomonas poae	strain=LMG 21465	GCA_001730605.1	200451	200451	type	True	85.3699	1274	2150	95	below_threshold
Pseudomonas kitaguniensis	strain=MAFF 212408	GCA_009296165.1	2607908	2607908	type	True	85.261	1228	2150	95	below_threshold
Pseudomonas laurentiana	strain=JCM 32154	GCA_014648275.1	2364649	2364649	type	True	80.6051	773	2150	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	79.4414	635	2150	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	79.3645	664	2150	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	78.7565	523	2150	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	75.8939	55	2150	95	below_threshold
Chitinimonas arctica	strain=R3-44	GCA_007431345.1	2594795	2594795	type	True	75.6237	81	2150	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	75.3508	96	2150	95	below_threshold
Caballeronia glathei	strain=DSM 50014	GCA_000698595.1	60547	60547	type	True	75.3269	97	2150	95	below_threshold
Caballeronia glathei	strain=LMG 14190	GCA_000751215.2	60547	60547	type	True	75.312	95	2150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:55,028] [INFO] DFAST Taxonomy check result was written to GCF_009724245.1_ASM972424v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:55,028] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:55,028] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:55,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca73edcd-6bf3-4893-a0cb-1fe081967f9d/dqc_reference/checkm_data
[2024-01-25 19:04:55,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:55,089] [INFO] Task started: CheckM
[2024-01-25 19:04:55,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009724245.1_ASM972424v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009724245.1_ASM972424v1_genomic.fna/checkm_input GCF_009724245.1_ASM972424v1_genomic.fna/checkm_result
[2024-01-25 19:05:55,406] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:55,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:55,424] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:55,424] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:55,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009724245.1_ASM972424v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:55,425] [INFO] Task started: Blastn
[2024-01-25 19:05:55,425] [INFO] Running command: blastn -query GCF_009724245.1_ASM972424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca73edcd-6bf3-4893-a0cb-1fe081967f9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009724245.1_ASM972424v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:56,768] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:56,771] [INFO] Selected 25 target genomes.
[2024-01-25 19:05:56,772] [INFO] Target genome list was writen to GCF_009724245.1_ASM972424v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:56,795] [INFO] Task started: fastANI
[2024-01-25 19:05:56,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fe6901d-4596-409d-bf7b-23e7b929a655/GCF_009724245.1_ASM972424v1_genomic.fna.gz --refList GCF_009724245.1_ASM972424v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009724245.1_ASM972424v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:33,592] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:33,607] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:33,608] [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_013403585.1	s__Pseudomonas_E yamanorum_B	98.3182	1915	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.31	98.31	0.89	0.89	2	conclusive
GCF_012935695.1	s__Pseudomonas_E sp012935695	93.3713	1849	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614655.1	s__Pseudomonas_E fluorescens_BX	92.6782	1647	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707515.1	s__Pseudomonas_E sp009707515	88.0887	1402	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013386765.1	s__Pseudomonas_E yamanorum_A	87.8941	1587	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.16	0.94	0.91	5	-
GCF_002204795.1	s__Pseudomonas_E sp002204795	87.7703	1545	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013386825.1	s__Pseudomonas_E sp013386825	87.6885	1567	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002874965.1	s__Pseudomonas_E sp002874965	87.6785	1618	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.46	0.92	0.88	48	-
GCF_008369295.1	s__Pseudomonas_E sp008369295	87.2692	1451	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.98	99.98	0.99	0.99	2	-
GCF_012985465.1	s__Pseudomonas_E sp012985465	86.5833	1443	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.94	0.91	0.90	5	-
GCF_007858285.1	s__Pseudomonas_E brenneri	86.5119	1468	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	97.33	0.94	0.88	10	-
GCF_900105325.1	s__Pseudomonas_E marginalis	86.1395	1509	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_014207255.1	s__Pseudomonas_E sp014207255	86.0973	1462	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.31	98.90	0.95	0.91	5	-
GCF_009866765.1	s__Pseudomonas_E sp009866765	86.0725	1436	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647715.1	s__Pseudomonas_E antarctica_A	86.0398	1527	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.45	0.91	0.91	2	-
GCF_900624995.1	s__Pseudomonas_E antarctica	85.8882	1410	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.98	99.98	1.00	1.00	3	-
GCF_001439815.1	s__Pseudomonas_E orientalis	85.6881	1388	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.01	96.05	0.91	0.89	6	-
GCF_002018875.1	s__Pseudomonas_E sp002018875	83.8825	1350	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.08	96.52	0.93	0.90	4	-
GCF_900105155.1	s__Pseudomonas_E prosekii	83.3457	1192	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	96.34	0.92	0.89	8	-
GCF_001043055.1	s__Pseudomonas_E weihenstephanensis	81.2925	844	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.02	97.13	0.92	0.88	6	-
GCF_900589395.1	s__Pseudomonas_E sp900589395	80.6587	879	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.16	0.94	0.93	8	-
GCF_014648275.1	s__Pseudomonas_E laurentiana	80.6208	771	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.92	99.92	0.99	0.99	2	-
GCF_002087235.1	s__Pseudomonas_E floridensis	80.5636	793	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013178375.1	s__Ch67 sp013178375	76.1761	132	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ch67	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	75.5419	69	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:33,610] [INFO] GTDB search result was written to GCF_009724245.1_ASM972424v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:33,611] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:33,616] [INFO] DFAST_QC result json was written to GCF_009724245.1_ASM972424v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:33,616] [INFO] DFAST_QC completed!
[2024-01-25 19:06:33,616] [INFO] Total running time: 0h2m43s