[2023-06-29 21:41:49,925] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:41:49,927] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:41:49,927] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3a349d6-24f1-4436-a909-3a2beb04d61b/dqc_reference
[2023-06-29 21:41:51,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:41:51,176] [INFO] Task started: Prodigal
[2023-06-29 21:41:51,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg08240f82-f948-4fac-84e8-2533c1370e5f/GCA_024102775.1_ASM2410277v1_genomic.fna.gz | prodigal -d GCA_024102775.1_ASM2410277v1_genomic.fna/cds.fna -a GCA_024102775.1_ASM2410277v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:42:02,362] [INFO] Task succeeded: Prodigal
[2023-06-29 21:42:02,363] [INFO] Task started: HMMsearch
[2023-06-29 21:42:02,363] [INFO] Running command: hmmsearch --tblout GCA_024102775.1_ASM2410277v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3a349d6-24f1-4436-a909-3a2beb04d61b/dqc_reference/reference_markers.hmm GCA_024102775.1_ASM2410277v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:42:02,668] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:42:02,670] [INFO] Found 6/6 markers.
[2023-06-29 21:42:02,718] [INFO] Query marker FASTA was written to GCA_024102775.1_ASM2410277v1_genomic.fna/markers.fasta
[2023-06-29 21:42:02,719] [INFO] Task started: Blastn
[2023-06-29 21:42:02,719] [INFO] Running command: blastn -query GCA_024102775.1_ASM2410277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3a349d6-24f1-4436-a909-3a2beb04d61b/dqc_reference/reference_markers.fasta -out GCA_024102775.1_ASM2410277v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:42:03,390] [INFO] Task succeeded: Blastn
[2023-06-29 21:42:03,395] [INFO] Selected 25 target genomes.
[2023-06-29 21:42:03,395] [INFO] Target genome list was writen to GCA_024102775.1_ASM2410277v1_genomic.fna/target_genomes.txt
[2023-06-29 21:42:03,398] [INFO] Task started: fastANI
[2023-06-29 21:42:03,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg08240f82-f948-4fac-84e8-2533c1370e5f/GCA_024102775.1_ASM2410277v1_genomic.fna.gz --refList GCA_024102775.1_ASM2410277v1_genomic.fna/target_genomes.txt --output GCA_024102775.1_ASM2410277v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:42:21,610] [INFO] Task succeeded: fastANI
[2023-06-29 21:42:21,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3a349d6-24f1-4436-a909-3a2beb04d61b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:42:21,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3a349d6-24f1-4436-a909-3a2beb04d61b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:42:21,626] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:42:21,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:42:21,627] [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
Aggregatilinea lenta	strain=MO-CFX2	GCA_003569045.1	913108	913108	type	True	75.7134	107	1237	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	75.0722	71	1237	95	below_threshold
Kitasatospora aureofaciens	strain=ATCC 10762	GCA_001188955.3	1894	1894	type	True	75.0244	73	1237	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	74.9332	61	1237	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.7832	66	1237	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	74.7602	51	1237	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	74.7051	84	1237	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:42:21,629] [INFO] DFAST Taxonomy check result was written to GCA_024102775.1_ASM2410277v1_genomic.fna/tc_result.tsv
[2023-06-29 21:42:21,630] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:42:21,630] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:42:21,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3a349d6-24f1-4436-a909-3a2beb04d61b/dqc_reference/checkm_data
[2023-06-29 21:42:21,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:42:21,675] [INFO] Task started: CheckM
[2023-06-29 21:42:21,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024102775.1_ASM2410277v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024102775.1_ASM2410277v1_genomic.fna/checkm_input GCA_024102775.1_ASM2410277v1_genomic.fna/checkm_result
[2023-06-29 21:42:58,590] [INFO] Task succeeded: CheckM
[2023-06-29 21:42:58,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:42:58,610] [INFO] ===== Completeness check finished =====
[2023-06-29 21:42:58,610] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:42:58,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024102775.1_ASM2410277v1_genomic.fna/markers.fasta)
[2023-06-29 21:42:58,611] [INFO] Task started: Blastn
[2023-06-29 21:42:58,611] [INFO] Running command: blastn -query GCA_024102775.1_ASM2410277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3a349d6-24f1-4436-a909-3a2beb04d61b/dqc_reference/reference_markers_gtdb.fasta -out GCA_024102775.1_ASM2410277v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:42:59,622] [INFO] Task succeeded: Blastn
[2023-06-29 21:42:59,626] [INFO] Selected 22 target genomes.
[2023-06-29 21:42:59,627] [INFO] Target genome list was writen to GCA_024102775.1_ASM2410277v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:42:59,641] [INFO] Task started: fastANI
[2023-06-29 21:42:59,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg08240f82-f948-4fac-84e8-2533c1370e5f/GCA_024102775.1_ASM2410277v1_genomic.fna.gz --refList GCA_024102775.1_ASM2410277v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024102775.1_ASM2410277v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:43:18,305] [INFO] Task succeeded: fastANI
[2023-06-29 21:43:18,322] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:43:18,322] [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_001567485.1	s__OLB13 sp001567485	99.2431	1147	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB13	95.0	99.21	98.90	0.94	0.92	9	conclusive
GCA_016716525.1	s__OLB13 sp016716525	84.4463	1110	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712885.1	s__OLB13 sp016712885	77.1119	313	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717205.1	s__OLB15 sp016717205	75.9988	140	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	97.47	97.38	0.90	0.87	3	-
GCA_013360465.1	s__OLB15 sp013360465	75.9037	137	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879865.1	s__OLB15 sp014879865	75.8056	120	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693385.1	s__J038 sp007693385	75.7261	76	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__J038	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864435.1	s__CFX2 sp903864435	75.7116	70	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789005.1	s__OLB15 sp016789005	75.6577	114	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432315.1	s__LM3-B42 sp018432315	75.5486	116	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__LM3-B42	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729765.1	s__JAAYCM01 sp012729765	75.5212	99	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__JAAYCM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385675.1	s__UBA3940 sp002385675	75.5027	60	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__UBA3940;g__UBA3940	95.0	99.28	99.28	0.83	0.83	2	-
GCA_011367385.1	s__SpSt-583 sp011367385	75.144	52	1237	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__SpSt-583	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:43:18,324] [INFO] GTDB search result was written to GCA_024102775.1_ASM2410277v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:43:18,325] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:43:18,329] [INFO] DFAST_QC result json was written to GCA_024102775.1_ASM2410277v1_genomic.fna/dqc_result.json
[2023-06-29 21:43:18,329] [INFO] DFAST_QC completed!
[2023-06-29 21:43:18,329] [INFO] Total running time: 0h1m28s