[2024-01-25 18:13:20,453] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:20,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:20,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d0660be-c103-4c92-a901-7d7b3d58c091/dqc_reference
[2024-01-25 18:13:21,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:21,611] [INFO] Task started: Prodigal
[2024-01-25 18:13:21,611] [INFO] Running command: gunzip -c /var/lib/cwl/stg450d9a74-eddf-438e-96af-46fee326179f/GCF_000160775.2_ASM16077v2_genomic.fna.gz | prodigal -d GCF_000160775.2_ASM16077v2_genomic.fna/cds.fna -a GCF_000160775.2_ASM16077v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:29,848] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:29,848] [INFO] Task started: HMMsearch
[2024-01-25 18:13:29,848] [INFO] Running command: hmmsearch --tblout GCF_000160775.2_ASM16077v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d0660be-c103-4c92-a901-7d7b3d58c091/dqc_reference/reference_markers.hmm GCF_000160775.2_ASM16077v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:30,062] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:30,063] [INFO] Found 6/6 markers.
[2024-01-25 18:13:30,090] [INFO] Query marker FASTA was written to GCF_000160775.2_ASM16077v2_genomic.fna/markers.fasta
[2024-01-25 18:13:30,090] [INFO] Task started: Blastn
[2024-01-25 18:13:30,090] [INFO] Running command: blastn -query GCF_000160775.2_ASM16077v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d0660be-c103-4c92-a901-7d7b3d58c091/dqc_reference/reference_markers.fasta -out GCF_000160775.2_ASM16077v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:31,213] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:31,215] [INFO] Selected 20 target genomes.
[2024-01-25 18:13:31,216] [INFO] Target genome list was writen to GCF_000160775.2_ASM16077v2_genomic.fna/target_genomes.txt
[2024-01-25 18:13:31,223] [INFO] Task started: fastANI
[2024-01-25 18:13:31,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg450d9a74-eddf-438e-96af-46fee326179f/GCF_000160775.2_ASM16077v2_genomic.fna.gz --refList GCF_000160775.2_ASM16077v2_genomic.fna/target_genomes.txt --output GCF_000160775.2_ASM16077v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:47,079] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:47,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d0660be-c103-4c92-a901-7d7b3d58c091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:47,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d0660be-c103-4c92-a901-7d7b3d58c091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:47,091] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:47,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:47,091] [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
Aeromicrobium marinum	strain=DSM 15272	GCA_000160775.2	219314	219314	type	True	100.0	1026	1026	95	conclusive
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	80.6974	563	1026	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	80.5638	570	1026	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	80.5409	515	1026	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	80.526	560	1026	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	80.4372	517	1026	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	80.304	469	1026	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	80.2142	448	1026	95	below_threshold
Aeromicrobium yanjiei	strain=MF47	GCA_009649075.1	2662028	2662028	type	True	80.2111	530	1026	95	below_threshold
Aeromicrobium erythreum	strain=AR18	GCA_001509405.1	2041	2041	type	True	80.2075	547	1026	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	80.1392	501	1026	95	below_threshold
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	80.1091	536	1026	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	80.0738	472	1026	95	below_threshold
Aeromicrobium phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	79.9511	464	1026	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	78.3513	407	1026	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	78.2698	328	1026	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	78.0399	411	1026	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.0151	361	1026	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	77.9233	376	1026	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	77.8966	352	1026	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:47,092] [INFO] DFAST Taxonomy check result was written to GCF_000160775.2_ASM16077v2_genomic.fna/tc_result.tsv
[2024-01-25 18:13:47,093] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:47,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:47,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d0660be-c103-4c92-a901-7d7b3d58c091/dqc_reference/checkm_data
[2024-01-25 18:13:47,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:47,127] [INFO] Task started: CheckM
[2024-01-25 18:13:47,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000160775.2_ASM16077v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000160775.2_ASM16077v2_genomic.fna/checkm_input GCF_000160775.2_ASM16077v2_genomic.fna/checkm_result
[2024-01-25 18:14:49,363] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:49,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:49,382] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:49,382] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:49,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000160775.2_ASM16077v2_genomic.fna/markers.fasta)
[2024-01-25 18:14:49,383] [INFO] Task started: Blastn
[2024-01-25 18:14:49,383] [INFO] Running command: blastn -query GCF_000160775.2_ASM16077v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d0660be-c103-4c92-a901-7d7b3d58c091/dqc_reference/reference_markers_gtdb.fasta -out GCF_000160775.2_ASM16077v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:51,206] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:51,209] [INFO] Selected 16 target genomes.
[2024-01-25 18:14:51,209] [INFO] Target genome list was writen to GCF_000160775.2_ASM16077v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:51,222] [INFO] Task started: fastANI
[2024-01-25 18:14:51,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg450d9a74-eddf-438e-96af-46fee326179f/GCF_000160775.2_ASM16077v2_genomic.fna.gz --refList GCF_000160775.2_ASM16077v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000160775.2_ASM16077v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:03,436] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:03,450] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:03,450] [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_000160775.2	s__Aeromicrobium marinum	100.0	1026	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000471045.1	s__Aeromicrobium sp000471045	81.6321	575	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426485.1	s__Aeromicrobium sp001426485	80.868	558	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.44	97.44	0.91	0.91	2	-
GCF_013283745.1	s__Aeromicrobium sp013283745	80.553	570	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003065605.1	s__Aeromicrobium chenweiae	80.4952	519	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873655.1	s__Aeromicrobium sp014873655	80.4301	522	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039565.1	s__Aeromicrobium terrae	80.429	518	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428805.1	s__Aeromicrobium sp001428805	80.4203	555	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408555.1	s__Aeromicrobium tamlense	80.3364	466	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009649075.1	s__Aeromicrobium yanjiei	80.2282	528	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.81	98.81	0.96	0.95	3	-
GCF_001509405.1	s__Aeromicrobium erythreum	80.2183	546	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.57	98.39	0.93	0.92	6	-
GCF_001423335.1	s__Aeromicrobium sp001423335	80.1891	545	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.72	97.77	0.96	0.93	5	-
GCF_900167475.1	s__Aeromicrobium choanae	80.1703	452	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994095.1	s__Mumia xiangluensis	78.4	391	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_014127485.1	s__Nocardioides sp014127485	78.2923	415	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_011046535.1	s__Nocardioides anomalus	77.919	402	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:03,453] [INFO] GTDB search result was written to GCF_000160775.2_ASM16077v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:03,453] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:03,456] [INFO] DFAST_QC result json was written to GCF_000160775.2_ASM16077v2_genomic.fna/dqc_result.json
[2024-01-25 18:15:03,457] [INFO] DFAST_QC completed!
[2024-01-25 18:15:03,457] [INFO] Total running time: 0h1m43s