[2024-01-25 20:14:05,802] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:05,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:05,803] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc904dc8-5b14-4520-a0b6-5cb2f3520681/dqc_reference
[2024-01-25 20:14:06,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:06,936] [INFO] Task started: Prodigal
[2024-01-25 20:14:06,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg932ac967-7536-4b45-a341-9b1b68d198b2/GCF_001043975.1_ASM104397v1_genomic.fna.gz | prodigal -d GCF_001043975.1_ASM104397v1_genomic.fna/cds.fna -a GCF_001043975.1_ASM104397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:22,533] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:22,533] [INFO] Task started: HMMsearch
[2024-01-25 20:14:22,533] [INFO] Running command: hmmsearch --tblout GCF_001043975.1_ASM104397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc904dc8-5b14-4520-a0b6-5cb2f3520681/dqc_reference/reference_markers.hmm GCF_001043975.1_ASM104397v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:22,875] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:22,877] [INFO] Found 6/6 markers.
[2024-01-25 20:14:22,936] [INFO] Query marker FASTA was written to GCF_001043975.1_ASM104397v1_genomic.fna/markers.fasta
[2024-01-25 20:14:22,937] [INFO] Task started: Blastn
[2024-01-25 20:14:22,937] [INFO] Running command: blastn -query GCF_001043975.1_ASM104397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc904dc8-5b14-4520-a0b6-5cb2f3520681/dqc_reference/reference_markers.fasta -out GCF_001043975.1_ASM104397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:23,991] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:23,994] [INFO] Selected 11 target genomes.
[2024-01-25 20:14:23,994] [INFO] Target genome list was writen to GCF_001043975.1_ASM104397v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:23,998] [INFO] Task started: fastANI
[2024-01-25 20:14:23,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg932ac967-7536-4b45-a341-9b1b68d198b2/GCF_001043975.1_ASM104397v1_genomic.fna.gz --refList GCF_001043975.1_ASM104397v1_genomic.fna/target_genomes.txt --output GCF_001043975.1_ASM104397v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:46,189] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:46,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc904dc8-5b14-4520-a0b6-5cb2f3520681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:46,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc904dc8-5b14-4520-a0b6-5cb2f3520681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:46,198] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:46,198] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:46,198] [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
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	100.0	2213	2234	95	conclusive
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	90.0693	1488	2234	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	89.9838	1645	2234	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	89.7898	1637	2234	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	89.5767	1499	2234	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	89.5655	1392	2234	95	below_threshold
Methylobacterium frigidaeris	strain=IER25-16	GCA_002759055.1	2038277	2038277	type	True	89.365	1030	2234	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	89.3369	1618	2234	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	89.1721	1595	2234	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	85.4466	1399	2234	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	84.7423	1296	2234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:46,199] [INFO] DFAST Taxonomy check result was written to GCF_001043975.1_ASM104397v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:46,200] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:46,200] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:46,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc904dc8-5b14-4520-a0b6-5cb2f3520681/dqc_reference/checkm_data
[2024-01-25 20:14:46,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:46,273] [INFO] Task started: CheckM
[2024-01-25 20:14:46,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001043975.1_ASM104397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001043975.1_ASM104397v1_genomic.fna/checkm_input GCF_001043975.1_ASM104397v1_genomic.fna/checkm_result
[2024-01-25 20:15:37,976] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:37,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:37,995] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:37,995] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:37,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001043975.1_ASM104397v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:37,996] [INFO] Task started: Blastn
[2024-01-25 20:15:37,996] [INFO] Running command: blastn -query GCF_001043975.1_ASM104397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc904dc8-5b14-4520-a0b6-5cb2f3520681/dqc_reference/reference_markers_gtdb.fasta -out GCF_001043975.1_ASM104397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:40,194] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:40,197] [INFO] Selected 10 target genomes.
[2024-01-25 20:15:40,197] [INFO] Target genome list was writen to GCF_001043975.1_ASM104397v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:40,202] [INFO] Task started: fastANI
[2024-01-25 20:15:40,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg932ac967-7536-4b45-a341-9b1b68d198b2/GCF_001043975.1_ASM104397v1_genomic.fna.gz --refList GCF_001043975.1_ASM104397v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001043975.1_ASM104397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:01,088] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:01,095] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:01,096] [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_001043975.1	s__Methylobacterium variabile	100.0	2213	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003173755.1	s__Methylobacterium terrae	90.0757	1487	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745635.1	s__Methylobacterium sp004745635	89.959	1648	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653715.1	s__Methylobacterium platani	89.5898	1497	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_003173775.1	s__Methylobacterium sp003173775	89.5779	1515	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_011043735.1	s__Methylobacterium sp011043735	89.5609	1599	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043955.1	s__Methylobacterium tarhaniae	89.5174	1397	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002759055.1	s__Methylobacterium frigidaeris	89.3759	1029	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058325.1	s__Methylobacterium currus	89.3427	1619	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151805.1	s__Methylobacterium sp006151805	89.2286	1589	2234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:01,097] [INFO] GTDB search result was written to GCF_001043975.1_ASM104397v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:01,097] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:01,101] [INFO] DFAST_QC result json was written to GCF_001043975.1_ASM104397v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:01,101] [INFO] DFAST_QC completed!
[2024-01-25 20:16:01,101] [INFO] Total running time: 0h1m55s