[2024-01-24 15:02:23,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,983] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cb5ccdc-3a93-4a3a-8e0d-8f4b8e061b94/dqc_reference
[2024-01-24 15:02:26,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,428] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg9368ebcd-1bd6-42ee-b7ff-65651cd0319b/GCF_003182475.1_ASM318247v1_genomic.fna.gz | prodigal -d GCF_003182475.1_ASM318247v1_genomic.fna/cds.fna -a GCF_003182475.1_ASM318247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:42,564] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:42,564] [INFO] Task started: HMMsearch
[2024-01-24 15:02:42,564] [INFO] Running command: hmmsearch --tblout GCF_003182475.1_ASM318247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cb5ccdc-3a93-4a3a-8e0d-8f4b8e061b94/dqc_reference/reference_markers.hmm GCF_003182475.1_ASM318247v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:42,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:42,953] [INFO] Found 6/6 markers.
[2024-01-24 15:02:43,001] [INFO] Query marker FASTA was written to GCF_003182475.1_ASM318247v1_genomic.fna/markers.fasta
[2024-01-24 15:02:43,002] [INFO] Task started: Blastn
[2024-01-24 15:02:43,002] [INFO] Running command: blastn -query GCF_003182475.1_ASM318247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cb5ccdc-3a93-4a3a-8e0d-8f4b8e061b94/dqc_reference/reference_markers.fasta -out GCF_003182475.1_ASM318247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:43,928] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:43,934] [INFO] Selected 25 target genomes.
[2024-01-24 15:02:43,935] [INFO] Target genome list was writen to GCF_003182475.1_ASM318247v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:43,964] [INFO] Task started: fastANI
[2024-01-24 15:02:43,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg9368ebcd-1bd6-42ee-b7ff-65651cd0319b/GCF_003182475.1_ASM318247v1_genomic.fna.gz --refList GCF_003182475.1_ASM318247v1_genomic.fna/target_genomes.txt --output GCF_003182475.1_ASM318247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:07,432] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:07,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cb5ccdc-3a93-4a3a-8e0d-8f4b8e061b94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:07,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cb5ccdc-3a93-4a3a-8e0d-8f4b8e061b94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:07,459] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:07,459] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:07,459] [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
Mangrovibacter plantisponsor	strain=DSM 19579	GCA_003182475.1	451513	451513	type	True	100.0	1750	1755	95	conclusive
Mangrovibacter phragmitis	strain=MP23	GCA_001655675.1	1691903	1691903	type	True	92.3946	1437	1755	95	below_threshold
Franconibacter daqui	strain=CGMCC 1.15944	GCA_014644275.1	2047724	2047724	type	True	79.2203	443	1755	95	below_threshold
Atlantibacter hermannii	strain=NBRC 105704	GCA_000248015.2	565	565	type	True	79.1335	406	1755	95	below_threshold
Atlantibacter hermannii	strain=FDAARGOS_888	GCA_016027855.1	565	565	type	True	79.1333	412	1755	95	below_threshold
Shimwellia blattae	strain=DSM 4481	GCA_000262305.1	563	563	type	True	79.093	401	1755	95	below_threshold
Shimwellia blattae	strain=NBRC 105725	GCA_000327265.1	563	563	type	True	79.0684	394	1755	95	below_threshold
Shimwellia pseudoproteus	strain=DSM 3038	GCA_016415625.1	570012	570012	type	True	79.0667	404	1755	95	below_threshold
Leclercia adecarboxylata	strain=NBRC 102595	GCA_001515505.1	83655	83655	suspected-type	True	79.0223	419	1755	95	below_threshold
Leclercia adecarboxylata	strain=FDAARGOS_1505	GCA_020097395.1	83655	83655	suspected-type	True	79.0053	421	1755	95	below_threshold
Leclercia adecarboxylata	strain=ATCC 23216	GCA_000735515.1	83655	83655	suspected-type	True	79.0037	405	1755	95	below_threshold
Escherichia fergusonii	strain=FDAARGOS_1499	GCA_020097475.1	564	564	type	True	78.9501	435	1755	95	below_threshold
Enterobacter ludwigii	strain=FDAARGOS 1436	GCA_019047005.1	299767	299767	type	True	78.9409	460	1755	95	below_threshold
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	78.9331	492	1755	95	below_threshold
Enterobacter ludwigii	strain=EN-119	GCA_001750725.1	299767	299767	type	True	78.9241	472	1755	95	below_threshold
Enterobacter ludwigii	strain=EN-119	GCA_000818595.1	299767	299767	type	True	78.9145	472	1755	95	below_threshold
Kosakonia oryzae	strain=CGMCC 1.7012	GCA_900112145.1	497725	497725	type	True	78.9058	498	1755	95	below_threshold
Lelliottia nimipressuralis	strain=CCUG 25894	GCA_004115925.1	69220	69220	type	True	78.862	422	1755	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	78.8393	465	1755	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	78.8304	424	1755	95	below_threshold
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	78.8259	407	1755	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	78.8259	423	1755	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.3363	225	1755	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	77.9825	260	1755	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	77.973	261	1755	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:07,461] [INFO] DFAST Taxonomy check result was written to GCF_003182475.1_ASM318247v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:07,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:07,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:07,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cb5ccdc-3a93-4a3a-8e0d-8f4b8e061b94/dqc_reference/checkm_data
[2024-01-24 15:03:07,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:07,517] [INFO] Task started: CheckM
[2024-01-24 15:03:07,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003182475.1_ASM318247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003182475.1_ASM318247v1_genomic.fna/checkm_input GCF_003182475.1_ASM318247v1_genomic.fna/checkm_result
[2024-01-24 15:03:56,757] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:56,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:56,779] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:56,779] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:56,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003182475.1_ASM318247v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:56,780] [INFO] Task started: Blastn
[2024-01-24 15:03:56,780] [INFO] Running command: blastn -query GCF_003182475.1_ASM318247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cb5ccdc-3a93-4a3a-8e0d-8f4b8e061b94/dqc_reference/reference_markers_gtdb.fasta -out GCF_003182475.1_ASM318247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:58,179] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:58,183] [INFO] Selected 22 target genomes.
[2024-01-24 15:03:58,183] [INFO] Target genome list was writen to GCF_003182475.1_ASM318247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:58,204] [INFO] Task started: fastANI
[2024-01-24 15:03:58,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg9368ebcd-1bd6-42ee-b7ff-65651cd0319b/GCF_003182475.1_ASM318247v1_genomic.fna.gz --refList GCF_003182475.1_ASM318247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003182475.1_ASM318247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:21,865] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:21,892] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:21,893] [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_003182475.1	s__Mangrovibacter plantisponsor	100.0	1750	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mangrovibacter	95.0	98.41	98.41	0.89	0.89	2	conclusive
GCF_001655675.1	s__Mangrovibacter phragmitis	92.4052	1436	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mangrovibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277175.1	s__Cronobacter universalis	79.1002	427	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCF_000262305.1	s__Shimwellia blattae	79.0986	402	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Shimwellia	95.0	99.99	99.99	1.00	1.00	4	-
GCF_007570865.1	s__Atlantibacter subterranea	79.0929	417	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.55	98.44	0.93	0.91	8	-
GCF_016415625.1	s__Shimwellia pseudoproteus	79.0504	405	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Shimwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902985.1	s__Leclercia sp002902985	78.9634	410	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.13	96.37	0.93	0.86	16	-
GCA_901472455.1	s__Leclercia adecarboxylata	78.9436	410	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.53	98.09	0.95	0.87	86	-
GCF_000410515.1	s__Kosakonia sp000410515	78.9414	473	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	98.63	98.59	0.96	0.95	5	-
GCF_001750725.1	s__Enterobacter ludwigii	78.9236	473	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.79	98.47	0.93	0.83	88	-
GCF_900978845.1	s__Klebsiella africana	78.9098	405	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_004115925.1	s__Lelliottia nimipressuralis	78.862	422	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.29	98.00	0.93	0.92	11	-
GCF_014193285.1	s__Atlantibacter sp002345315	78.8497	425	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.54	98.53	0.93	0.90	4	-
GCF_900094925.1	s__Kosakonia oryzendophytica	78.8393	465	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	99.59	99.37	0.98	0.97	4	-
GCF_009907385.1	s__Atlantibacter hermannii_A	78.8261	428	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000280495.2	s__Kosakonia radicincitans	78.824	498	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
GCF_001297775.1	s__Trabulsiella odontotermitis	78.8153	431	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Trabulsiella	95.0	99.98	99.97	0.99	0.99	5	-
GCA_001484765.1	s__Erwinia_A teleogrylli	78.8079	411	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759835.1	s__Citrobacter_A sedlakii	78.7671	419	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.16	99.00	0.95	0.93	10	-
GCF_011064845.1	s__Citrobacter freundii	78.7199	437	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.70	97.40	0.89	0.80	446	-
GCF_016756775.1	s__Buttiauxella davisae_A	78.7114	412	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900079995.3	s__Citrobacter europaeus	78.6646	449	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:21,895] [INFO] GTDB search result was written to GCF_003182475.1_ASM318247v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:21,895] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:21,901] [INFO] DFAST_QC result json was written to GCF_003182475.1_ASM318247v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:21,902] [INFO] DFAST_QC completed!
[2024-01-24 15:04:21,902] [INFO] Total running time: 0h1m58s