[2024-01-25 18:50:50,774] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:50,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:50,777] [INFO] DQC Reference Directory: /var/lib/cwl/stgaefcfd84-9f28-43c7-9bf9-ea5d04365a9e/dqc_reference
[2024-01-25 18:50:51,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:51,930] [INFO] Task started: Prodigal
[2024-01-25 18:50:51,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cd88e0a-39c7-48d0-b68f-67212e1a32d3/GCF_009602465.1_ASM960246v1_genomic.fna.gz | prodigal -d GCF_009602465.1_ASM960246v1_genomic.fna/cds.fna -a GCF_009602465.1_ASM960246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:01,118] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:01,118] [INFO] Task started: HMMsearch
[2024-01-25 18:51:01,118] [INFO] Running command: hmmsearch --tblout GCF_009602465.1_ASM960246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaefcfd84-9f28-43c7-9bf9-ea5d04365a9e/dqc_reference/reference_markers.hmm GCF_009602465.1_ASM960246v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:01,316] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:01,317] [INFO] Found 6/6 markers.
[2024-01-25 18:51:01,348] [INFO] Query marker FASTA was written to GCF_009602465.1_ASM960246v1_genomic.fna/markers.fasta
[2024-01-25 18:51:01,348] [INFO] Task started: Blastn
[2024-01-25 18:51:01,348] [INFO] Running command: blastn -query GCF_009602465.1_ASM960246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaefcfd84-9f28-43c7-9bf9-ea5d04365a9e/dqc_reference/reference_markers.fasta -out GCF_009602465.1_ASM960246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:02,490] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:02,492] [INFO] Selected 25 target genomes.
[2024-01-25 18:51:02,493] [INFO] Target genome list was writen to GCF_009602465.1_ASM960246v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:02,552] [INFO] Task started: fastANI
[2024-01-25 18:51:02,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cd88e0a-39c7-48d0-b68f-67212e1a32d3/GCF_009602465.1_ASM960246v1_genomic.fna.gz --refList GCF_009602465.1_ASM960246v1_genomic.fna/target_genomes.txt --output GCF_009602465.1_ASM960246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:29,417] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:29,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaefcfd84-9f28-43c7-9bf9-ea5d04365a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:29,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaefcfd84-9f28-43c7-9bf9-ea5d04365a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:29,432] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:51:29,432] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:51:29,432] [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
Cumulibacter soli	strain=G-1	GCA_004382795.1	2546344	2546344	type	True	78.6117	451	1235	95	below_threshold
Antricoccus suffuscus	strain=DSM 100065	GCA_003003235.1	1629062	1629062	type	True	77.8567	345	1235	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	77.5222	385	1235	95	below_threshold
Klenkia brasiliensis	strain=DSM 44526	GCA_900100695.1	333142	333142	type	True	77.3538	402	1235	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	77.184	336	1235	95	below_threshold
Klenkia taihuensis	strain=DSM 45962	GCA_900112525.1	1225127	1225127	type	True	77.1321	412	1235	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	77.1237	451	1235	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	77.0526	367	1235	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	77.0213	347	1235	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	76.9869	370	1235	95	below_threshold
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	76.9003	291	1235	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	76.8185	363	1235	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	76.7901	314	1235	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	76.7255	349	1235	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	76.6867	442	1235	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	76.6672	427	1235	95	below_threshold
Nocardioides jensenii	strain=NBRC 14755	GCA_001552535.1	1843	1843	type	True	76.6351	296	1235	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	76.623	372	1235	95	below_threshold
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	76.6217	355	1235	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	76.6021	374	1235	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	76.6021	276	1235	95	below_threshold
Mangrovactinospora gilvigriseus	strain=MUSC 26	GCA_001879105.1	1428644	1428644	type	True	76.5295	300	1235	95	below_threshold
Streptacidiphilus carbonis	strain=NBRC 100919	GCA_000787775.1	105422	105422	type	True	76.4271	329	1235	95	below_threshold
Amycolatopsis acidicola	strain=K81G1	GCA_007713735.2	2596893	2596893	type	True	76.3731	364	1235	95	below_threshold
Actinomadura harenae	strain=NEAU-Ht49	GCA_003696215.1	2483351	2483351	type	True	76.366	382	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:29,435] [INFO] DFAST Taxonomy check result was written to GCF_009602465.1_ASM960246v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:29,435] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:29,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:29,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaefcfd84-9f28-43c7-9bf9-ea5d04365a9e/dqc_reference/checkm_data
[2024-01-25 18:51:29,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:29,475] [INFO] Task started: CheckM
[2024-01-25 18:51:29,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009602465.1_ASM960246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009602465.1_ASM960246v1_genomic.fna/checkm_input GCF_009602465.1_ASM960246v1_genomic.fna/checkm_result
[2024-01-25 18:51:59,637] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:59,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:59,660] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:59,660] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:59,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009602465.1_ASM960246v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:59,660] [INFO] Task started: Blastn
[2024-01-25 18:51:59,661] [INFO] Running command: blastn -query GCF_009602465.1_ASM960246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaefcfd84-9f28-43c7-9bf9-ea5d04365a9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009602465.1_ASM960246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:01,483] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:01,487] [INFO] Selected 12 target genomes.
[2024-01-25 18:52:01,487] [INFO] Target genome list was writen to GCF_009602465.1_ASM960246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:01,500] [INFO] Task started: fastANI
[2024-01-25 18:52:01,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cd88e0a-39c7-48d0-b68f-67212e1a32d3/GCF_009602465.1_ASM960246v1_genomic.fna.gz --refList GCF_009602465.1_ASM960246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009602465.1_ASM960246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:12,593] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:12,602] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:12,602] [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_009602465.1	s__Cumulibacter manganitolerans	100.0	1227	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Cumulibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900292035.1	s__Cumulibacter sp900292035	81.9748	672	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Cumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834025.1	s__Epidermidibacterium keratini	79.858	584	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Epidermidibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004382795.1	s__Cumulibacter soli	78.6117	451	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Cumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003235.1	s__Antricoccus suffuscus	77.8888	341	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Antricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900221005.1	s__Blastococcus aggregatus	77.5305	384	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143215.1	s__Geodermatophilus obscurus_A	77.2305	416	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805565.1	s__CADCTP01 sp902805565	77.0716	342	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750215.1	s__Xylanimonas variabilis_A	76.8061	265	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552535.1	s__Nocardioides jensenii	76.6806	290	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	76.6297	278	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879105.1	s__Streptomyces_G gilvigriseus	76.5154	302	1235	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:12,603] [INFO] GTDB search result was written to GCF_009602465.1_ASM960246v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:12,604] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:12,607] [INFO] DFAST_QC result json was written to GCF_009602465.1_ASM960246v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:12,607] [INFO] DFAST_QC completed!
[2024-01-25 18:52:12,608] [INFO] Total running time: 0h1m22s