[2024-01-24 13:40:42,787] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg75eb0a73-696b-4c4b-ae9f-6310acce56c1/dqc_reference
[2024-01-24 13:40:44,163] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,164] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ea1a36c-0d33-410a-9c56-70b34b9d3821/GCF_006912135.1_ASM691213v1_genomic.fna.gz | prodigal -d GCF_006912135.1_ASM691213v1_genomic.fna/cds.fna -a GCF_006912135.1_ASM691213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:07,455] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:07,456] [INFO] Task started: HMMsearch
[2024-01-24 13:41:07,456] [INFO] Running command: hmmsearch --tblout GCF_006912135.1_ASM691213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75eb0a73-696b-4c4b-ae9f-6310acce56c1/dqc_reference/reference_markers.hmm GCF_006912135.1_ASM691213v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:07,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:07,947] [INFO] Found 6/6 markers.
[2024-01-24 13:41:08,013] [INFO] Query marker FASTA was written to GCF_006912135.1_ASM691213v1_genomic.fna/markers.fasta
[2024-01-24 13:41:08,014] [INFO] Task started: Blastn
[2024-01-24 13:41:08,014] [INFO] Running command: blastn -query GCF_006912135.1_ASM691213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75eb0a73-696b-4c4b-ae9f-6310acce56c1/dqc_reference/reference_markers.fasta -out GCF_006912135.1_ASM691213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:09,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:09,457] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:09,457] [INFO] Target genome list was writen to GCF_006912135.1_ASM691213v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:09,463] [INFO] Task started: fastANI
[2024-01-24 13:41:09,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea1a36c-0d33-410a-9c56-70b34b9d3821/GCF_006912135.1_ASM691213v1_genomic.fna.gz --refList GCF_006912135.1_ASM691213v1_genomic.fna/target_genomes.txt --output GCF_006912135.1_ASM691213v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:39,304] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:39,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75eb0a73-696b-4c4b-ae9f-6310acce56c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:39,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75eb0a73-696b-4c4b-ae9f-6310acce56c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:39,318] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:39,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:39,318] [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
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	100.0	2777	2780	95	conclusive
Cryptosporangium aurantiacum	strain=DSM 46144	GCA_900143005.1	134849	134849	type	True	83.1883	1763	2780	95	below_threshold
Cryptosporangium arvum	strain=DSM 44712	GCA_000585375.1	80871	80871	type	True	83.1816	1851	2780	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	76.5834	779	2780	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	76.4222	863	2780	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	76.4047	896	2780	95	below_threshold
Actinocatenispora sera	strain=NBRC 101916	GCA_018324685.1	390989	390989	type	True	76.377	784	2780	95	below_threshold
Actinocatenispora sera	strain=NRRL B-24477	GCA_000720965.1	390989	390989	type	True	76.3602	791	2780	95	below_threshold
Virgisporangium aurantiacum	strain=NBRC 16421	GCA_016863635.1	175570	175570	type	True	76.3517	1077	2780	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	76.2136	616	2780	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	76.1949	528	2780	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	76.181	694	2780	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	76.0511	670	2780	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	76.0231	664	2780	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	76.0153	656	2780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:39,320] [INFO] DFAST Taxonomy check result was written to GCF_006912135.1_ASM691213v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:39,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:39,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:39,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75eb0a73-696b-4c4b-ae9f-6310acce56c1/dqc_reference/checkm_data
[2024-01-24 13:41:39,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:39,407] [INFO] Task started: CheckM
[2024-01-24 13:41:39,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006912135.1_ASM691213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006912135.1_ASM691213v1_genomic.fna/checkm_input GCF_006912135.1_ASM691213v1_genomic.fna/checkm_result
[2024-01-24 13:42:45,290] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:45,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:45,314] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:45,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:45,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006912135.1_ASM691213v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:45,315] [INFO] Task started: Blastn
[2024-01-24 13:42:45,316] [INFO] Running command: blastn -query GCF_006912135.1_ASM691213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75eb0a73-696b-4c4b-ae9f-6310acce56c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_006912135.1_ASM691213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:47,299] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:47,302] [INFO] Selected 15 target genomes.
[2024-01-24 13:42:47,302] [INFO] Target genome list was writen to GCF_006912135.1_ASM691213v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:47,377] [INFO] Task started: fastANI
[2024-01-24 13:42:47,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea1a36c-0d33-410a-9c56-70b34b9d3821/GCF_006912135.1_ASM691213v1_genomic.fna.gz --refList GCF_006912135.1_ASM691213v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006912135.1_ASM691213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:14,758] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:14,776] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:14,776] [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_006912135.1	s__Cryptosporangium phraense	100.0	2777	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900143005.1	s__Cryptosporangium aurantiacum	83.195	1761	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585375.1	s__Cryptosporangium arvum	83.1822	1852	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805565.1	s__CADCTP01 sp902805565	76.6542	630	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	76.6026	948	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862315.1	s__Actinoplanes palleronii	76.5823	989	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_900091605.1	s__Micromonospora tulbaghiae	76.5629	784	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_010993745.1	s__Fodinicola acaciae	76.5351	647	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__HKI-0501;g__Fodinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	76.422	891	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_018324685.1	s__Actinocatenispora sera	76.3669	787	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016863635.1	s__Virgisporangium aurantiacum	76.3636	1070	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	76.223	677	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200435.1	s__Sphaerisporangium krabiense	76.0609	667	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001995215.1	s__Amycolatopsis azurea	76.0574	646	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000424825.1	s__Streptomyces sp000424825	75.8211	538	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:14,779] [INFO] GTDB search result was written to GCF_006912135.1_ASM691213v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:14,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:14,783] [INFO] DFAST_QC result json was written to GCF_006912135.1_ASM691213v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:14,783] [INFO] DFAST_QC completed!
[2024-01-24 13:43:14,783] [INFO] Total running time: 0h2m32s