[2024-01-25 19:02:21,154] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:21,156] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:21,156] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fae3018-151b-4765-9292-52379f158607/dqc_reference
[2024-01-25 19:02:22,332] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:22,333] [INFO] Task started: Prodigal
[2024-01-25 19:02:22,333] [INFO] Running command: gunzip -c /var/lib/cwl/stgd254f88f-3361-4c1b-a1ad-bf6c03d2bac1/GCF_023806485.1_ASM2380648v1_genomic.fna.gz | prodigal -d GCF_023806485.1_ASM2380648v1_genomic.fna/cds.fna -a GCF_023806485.1_ASM2380648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:31,014] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:31,014] [INFO] Task started: HMMsearch
[2024-01-25 19:02:31,014] [INFO] Running command: hmmsearch --tblout GCF_023806485.1_ASM2380648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fae3018-151b-4765-9292-52379f158607/dqc_reference/reference_markers.hmm GCF_023806485.1_ASM2380648v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:31,232] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:31,233] [INFO] Found 6/6 markers.
[2024-01-25 19:02:31,273] [INFO] Query marker FASTA was written to GCF_023806485.1_ASM2380648v1_genomic.fna/markers.fasta
[2024-01-25 19:02:31,274] [INFO] Task started: Blastn
[2024-01-25 19:02:31,274] [INFO] Running command: blastn -query GCF_023806485.1_ASM2380648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fae3018-151b-4765-9292-52379f158607/dqc_reference/reference_markers.fasta -out GCF_023806485.1_ASM2380648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:31,877] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:31,880] [INFO] Selected 20 target genomes.
[2024-01-25 19:02:31,881] [INFO] Target genome list was writen to GCF_023806485.1_ASM2380648v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:31,909] [INFO] Task started: fastANI
[2024-01-25 19:02:31,910] [INFO] Running command: fastANI --query /var/lib/cwl/stgd254f88f-3361-4c1b-a1ad-bf6c03d2bac1/GCF_023806485.1_ASM2380648v1_genomic.fna.gz --refList GCF_023806485.1_ASM2380648v1_genomic.fna/target_genomes.txt --output GCF_023806485.1_ASM2380648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:46,642] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:46,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fae3018-151b-4765-9292-52379f158607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:46,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fae3018-151b-4765-9292-52379f158607/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:46,653] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:02:46,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:02:46,654] [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
Thermomicrobium roseum	strain=DSM 5159	GCA_000021685.1	500	500	type	True	77.0287	156	1187	95	below_threshold
Sphaerobacter thermophilus	strain=DSM 20745	GCA_000024985.1	2057	2057	type	True	76.9769	255	1187	95	below_threshold
Nitrolancea hollandica	strain=Lb	GCA_000297255.1	1206749	1206749	type	True	76.1618	83	1187	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.9543	61	1187	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	74.9391	63	1187	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	74.9229	65	1187	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	74.9009	77	1187	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	74.8796	78	1187	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	74.7952	77	1187	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	74.7926	51	1187	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.7865	76	1187	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	74.7772	54	1187	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	74.7722	56	1187	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	74.7667	57	1187	95	below_threshold
Burkholderia gladioli	strain=NBRC 13700	GCA_000739755.1	28095	28095	type	True	74.7621	116	1187	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	74.7567	85	1187	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	74.6922	55	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:46,655] [INFO] DFAST Taxonomy check result was written to GCF_023806485.1_ASM2380648v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:46,655] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:46,656] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:46,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fae3018-151b-4765-9292-52379f158607/dqc_reference/checkm_data
[2024-01-25 19:02:46,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:46,693] [INFO] Task started: CheckM
[2024-01-25 19:02:46,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023806485.1_ASM2380648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023806485.1_ASM2380648v1_genomic.fna/checkm_input GCF_023806485.1_ASM2380648v1_genomic.fna/checkm_result
[2024-01-25 19:03:14,006] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:14,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:14,026] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:14,026] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:14,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023806485.1_ASM2380648v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:14,027] [INFO] Task started: Blastn
[2024-01-25 19:03:14,027] [INFO] Running command: blastn -query GCF_023806485.1_ASM2380648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fae3018-151b-4765-9292-52379f158607/dqc_reference/reference_markers_gtdb.fasta -out GCF_023806485.1_ASM2380648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:15,022] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:15,025] [INFO] Selected 17 target genomes.
[2024-01-25 19:03:15,025] [INFO] Target genome list was writen to GCF_023806485.1_ASM2380648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:15,064] [INFO] Task started: fastANI
[2024-01-25 19:03:15,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgd254f88f-3361-4c1b-a1ad-bf6c03d2bac1/GCF_023806485.1_ASM2380648v1_genomic.fna.gz --refList GCF_023806485.1_ASM2380648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023806485.1_ASM2380648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:25,204] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:25,211] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:25,211] [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_011054265.1	s__HRBIN26 sp011054265	96.6632	760	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__HRBIN26	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002898875.1	s__HRBIN26 sp002898875	86.9286	661	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__HRBIN26	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014874455.1	s__HRBIN26 sp014874455	83.6763	797	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__HRBIN26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021685.1	s__Thermomicrobium roseum	77.0287	156	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Thermomicrobium	95.0	98.52	98.29	0.96	0.94	6	-
GCF_000024985.1	s__Sphaerobacter thermophilus	76.9779	253	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Sphaerobacter	95.0	99.04	99.02	0.92	0.89	3	-
GCA_002898975.1	s__Thermomicrobium sp002898975	76.9206	106	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Thermomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806345.1	s__CADCWF01 sp902806345	75.8805	113	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__CADCWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810765.1	s__CADDYR01 sp902810765	75.3581	66	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermobaculales;f__Thermobaculaceae;g__CADDYR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697005.1	s__JACCXM01 sp013697005	75.0149	54	1187	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__JACCXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011135.1	s__Rathayibacter festucae	74.7896	78	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	96.98	96.51	0.89	0.87	11	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:25,212] [INFO] GTDB search result was written to GCF_023806485.1_ASM2380648v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:25,213] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:25,216] [INFO] DFAST_QC result json was written to GCF_023806485.1_ASM2380648v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:25,216] [INFO] DFAST_QC completed!
[2024-01-25 19:03:25,216] [INFO] Total running time: 0h1m4s