[2024-01-25 19:37:05,723] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:05,725] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:05,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fbbf6dc-8b19-407c-a418-8efa2414669c/dqc_reference
[2024-01-25 19:37:06,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:06,915] [INFO] Task started: Prodigal
[2024-01-25 19:37:06,915] [INFO] Running command: gunzip -c /var/lib/cwl/stga8b47aea-dffa-47bf-b55b-df74de99dc1f/GCF_000721185.1_ASM72118v1_genomic.fna.gz | prodigal -d GCF_000721185.1_ASM72118v1_genomic.fna/cds.fna -a GCF_000721185.1_ASM72118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:26,539] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:26,539] [INFO] Task started: HMMsearch
[2024-01-25 19:37:26,539] [INFO] Running command: hmmsearch --tblout GCF_000721185.1_ASM72118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fbbf6dc-8b19-407c-a418-8efa2414669c/dqc_reference/reference_markers.hmm GCF_000721185.1_ASM72118v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:26,863] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:26,864] [INFO] Found 6/6 markers.
[2024-01-25 19:37:26,920] [INFO] Query marker FASTA was written to GCF_000721185.1_ASM72118v1_genomic.fna/markers.fasta
[2024-01-25 19:37:26,920] [INFO] Task started: Blastn
[2024-01-25 19:37:26,920] [INFO] Running command: blastn -query GCF_000721185.1_ASM72118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fbbf6dc-8b19-407c-a418-8efa2414669c/dqc_reference/reference_markers.fasta -out GCF_000721185.1_ASM72118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:28,121] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:28,125] [INFO] Selected 20 target genomes.
[2024-01-25 19:37:28,125] [INFO] Target genome list was writen to GCF_000721185.1_ASM72118v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:28,142] [INFO] Task started: fastANI
[2024-01-25 19:37:28,142] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b47aea-dffa-47bf-b55b-df74de99dc1f/GCF_000721185.1_ASM72118v1_genomic.fna.gz --refList GCF_000721185.1_ASM72118v1_genomic.fna/target_genomes.txt --output GCF_000721185.1_ASM72118v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:01,221] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:01,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fbbf6dc-8b19-407c-a418-8efa2414669c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:01,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fbbf6dc-8b19-407c-a418-8efa2414669c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:01,234] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:38:01,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:01,235] [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
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	100.0	2450	2453	95	conclusive
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	87.2328	1703	2453	95	below_threshold
Streptomyces nitrosporeus	strain=JCM 4598	GCA_014650375.1	28894	28894	type	True	87.148	1721	2453	95	below_threshold
Streptomyces clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	86.6578	1655	2453	95	below_threshold
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	86.629	1656	2453	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	86.2549	1650	2453	95	below_threshold
Streptomyces fulvorobeus	strain=NBRC 15897	GCA_013167895.1	284028	284028	type	True	84.9499	1393	2453	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	84.9464	1383	2453	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	84.6917	1454	2453	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	84.6429	1516	2453	95	below_threshold
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	84.5171	1457	2453	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.9637	996	2453	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.6775	1036	2453	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.3009	1300	2453	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	80.9547	1306	2453	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	74.8587	298	2453	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.8248	315	2453	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.8204	292	2453	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	74.8019	276	2453	95	below_threshold
Bradymonas sediminis	strain=FA350	GCA_003258315.1	1548548	1548548	type	True	74.6551	56	2453	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:01,236] [INFO] DFAST Taxonomy check result was written to GCF_000721185.1_ASM72118v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:01,237] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:01,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:01,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fbbf6dc-8b19-407c-a418-8efa2414669c/dqc_reference/checkm_data
[2024-01-25 19:38:01,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:01,307] [INFO] Task started: CheckM
[2024-01-25 19:38:01,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000721185.1_ASM72118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000721185.1_ASM72118v1_genomic.fna/checkm_input GCF_000721185.1_ASM72118v1_genomic.fna/checkm_result
[2024-01-25 19:39:46,569] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:46,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.54%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:46,590] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:46,591] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:46,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000721185.1_ASM72118v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:46,595] [INFO] Task started: Blastn
[2024-01-25 19:39:46,595] [INFO] Running command: blastn -query GCF_000721185.1_ASM72118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fbbf6dc-8b19-407c-a418-8efa2414669c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000721185.1_ASM72118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:48,583] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:48,585] [INFO] Selected 15 target genomes.
[2024-01-25 19:39:48,586] [INFO] Target genome list was writen to GCF_000721185.1_ASM72118v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:48,596] [INFO] Task started: fastANI
[2024-01-25 19:39:48,596] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b47aea-dffa-47bf-b55b-df74de99dc1f/GCF_000721185.1_ASM72118v1_genomic.fna.gz --refList GCF_000721185.1_ASM72118v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000721185.1_ASM72118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:19,816] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:19,828] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:19,833] [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_000720535.1	s__Streptomyces halstedii	99.9911	2448	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	96.54	0.92	0.83	17	conclusive
GCF_000177195.2	s__Streptomyces sp000177195	90.0575	1857	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.71	97.52	0.98	0.91	17	-
GCF_008704555.1	s__Streptomyces nitrosporeus	87.202	1707	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.98	0.98	2	-
GCA_014651175.1	s__Streptomyces clavifer	86.6616	1652	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.32	0.96	0.94	5	-
GCF_002910915.1	s__Streptomyces sp002910915	86.5038	1518	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905505.1	s__Streptomyces sp001905505	86.4761	1710	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002941025.1	s__Streptomyces sp002941025	86.4604	1705	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001715295.1	s__Streptomyces griseus_G	86.295	1550	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700505.1	s__Streptomyces mutomycini	86.2595	1495	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.53	0.96	0.96	2	-
GCF_007829855.1	s__Streptomyces argenteolus	86.0937	1645	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905735.1	s__Streptomyces sp001905735	84.5226	1560	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	95.22	0.92	0.85	6	-
GCF_014650175.1	s__Streptomyces termitum	82.1379	1301	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649335.1	s__Streptomyces roseolilacinus	81.968	1248	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719865.1	s__Streptomyces albus_E	80.7898	1111	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	78.7835	910	2453	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:19,834] [INFO] GTDB search result was written to GCF_000721185.1_ASM72118v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:19,835] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:19,838] [INFO] DFAST_QC result json was written to GCF_000721185.1_ASM72118v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:19,838] [INFO] DFAST_QC completed!
[2024-01-25 19:40:19,838] [INFO] Total running time: 0h3m14s