[2024-01-24 12:14:48,962] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,964] [INFO] DQC Reference Directory: /var/lib/cwl/stgff84134d-1bdd-4a28-9c6c-9f284343d505/dqc_reference
[2024-01-24 12:14:50,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,400] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,400] [INFO] Running command: gunzip -c /var/lib/cwl/stg66c1cf03-8ab7-4c61-82c2-fd17c678d7c0/GCF_003574465.1_ASM357446v1_genomic.fna.gz | prodigal -d GCF_003574465.1_ASM357446v1_genomic.fna/cds.fna -a GCF_003574465.1_ASM357446v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:07,503] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:07,504] [INFO] Task started: HMMsearch
[2024-01-24 12:15:07,504] [INFO] Running command: hmmsearch --tblout GCF_003574465.1_ASM357446v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff84134d-1bdd-4a28-9c6c-9f284343d505/dqc_reference/reference_markers.hmm GCF_003574465.1_ASM357446v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:07,918] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:07,920] [INFO] Found 6/6 markers.
[2024-01-24 12:15:07,987] [INFO] Query marker FASTA was written to GCF_003574465.1_ASM357446v1_genomic.fna/markers.fasta
[2024-01-24 12:15:07,987] [INFO] Task started: Blastn
[2024-01-24 12:15:07,987] [INFO] Running command: blastn -query GCF_003574465.1_ASM357446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff84134d-1bdd-4a28-9c6c-9f284343d505/dqc_reference/reference_markers.fasta -out GCF_003574465.1_ASM357446v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:09,123] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:09,127] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:09,127] [INFO] Target genome list was writen to GCF_003574465.1_ASM357446v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:09,134] [INFO] Task started: fastANI
[2024-01-24 12:15:09,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg66c1cf03-8ab7-4c61-82c2-fd17c678d7c0/GCF_003574465.1_ASM357446v1_genomic.fna.gz --refList GCF_003574465.1_ASM357446v1_genomic.fna/target_genomes.txt --output GCF_003574465.1_ASM357446v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:34,152] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:34,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff84134d-1bdd-4a28-9c6c-9f284343d505/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:34,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff84134d-1bdd-4a28-9c6c-9f284343d505/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:34,167] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:34,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:34,167] [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 crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	100.0	2269	2295	95	conclusive
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	99.9767	2269	2295	95	conclusive
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	85.4898	1337	2295	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	85.3188	1356	2295	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	85.2734	1484	2295	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	84.9035	1304	2295	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	84.828	1478	2295	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	84.8151	1276	2295	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	84.7228	1459	2295	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	84.6633	1421	2295	95	below_threshold
Methylobacterium frigidaeris	strain=IER25-16	GCA_002759055.1	2038277	2038277	type	True	84.6079	949	2295	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	84.0877	1318	2295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:34,169] [INFO] DFAST Taxonomy check result was written to GCF_003574465.1_ASM357446v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:34,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:34,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:34,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff84134d-1bdd-4a28-9c6c-9f284343d505/dqc_reference/checkm_data
[2024-01-24 12:15:34,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:34,239] [INFO] Task started: CheckM
[2024-01-24 12:15:34,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574465.1_ASM357446v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574465.1_ASM357446v1_genomic.fna/checkm_input GCF_003574465.1_ASM357446v1_genomic.fna/checkm_result
[2024-01-24 12:16:49,777] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:49,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:49,807] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:49,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:49,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574465.1_ASM357446v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:49,808] [INFO] Task started: Blastn
[2024-01-24 12:16:49,808] [INFO] Running command: blastn -query GCF_003574465.1_ASM357446v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff84134d-1bdd-4a28-9c6c-9f284343d505/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574465.1_ASM357446v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:51,932] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:51,936] [INFO] Selected 12 target genomes.
[2024-01-24 12:16:51,936] [INFO] Target genome list was writen to GCF_003574465.1_ASM357446v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:51,946] [INFO] Task started: fastANI
[2024-01-24 12:16:51,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg66c1cf03-8ab7-4c61-82c2-fd17c678d7c0/GCF_003574465.1_ASM357446v1_genomic.fna.gz --refList GCF_003574465.1_ASM357446v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003574465.1_ASM357446v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:15,609] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:15,620] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:15,620] [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_003574465.1	s__Methylobacterium crusticola	100.0	2269	2295	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_001043975.1	s__Methylobacterium variabile	85.466	1340	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173755.1	s__Methylobacterium terrae	85.3265	1353	2295	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	85.2386	1488	2295	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	85.1096	1380	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_016613415.1	s__Methylobacterium ajmalii	84.8952	1305	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.55	96.20	0.90	0.83	5	-
GCF_001043955.1	s__Methylobacterium tarhaniae	84.8547	1271	2295	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	84.6735	1466	2295	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	84.6628	1420	2295	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	84.5564	954	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016804325.1	s__Methylobacterium aquaticum_C	84.5029	1390	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019365.1	s__Methylobacterium sp000019365	83.2506	1342	2295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:15,622] [INFO] GTDB search result was written to GCF_003574465.1_ASM357446v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:15,623] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:15,626] [INFO] DFAST_QC result json was written to GCF_003574465.1_ASM357446v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:15,626] [INFO] DFAST_QC completed!
[2024-01-24 12:17:15,626] [INFO] Total running time: 0h2m27s