[2024-01-24 13:40:26,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:26,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:26,750] [INFO] DQC Reference Directory: /var/lib/cwl/stge5a4a558-d13f-4a04-a364-bf3884913363/dqc_reference
[2024-01-24 13:40:28,174] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:28,175] [INFO] Task started: Prodigal
[2024-01-24 13:40:28,175] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d1e09c9-cf8f-4062-9330-b5a86f75310c/GCF_002760665.1_ASM276066v1_genomic.fna.gz | prodigal -d GCF_002760665.1_ASM276066v1_genomic.fna/cds.fna -a GCF_002760665.1_ASM276066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:43,782] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:43,782] [INFO] Task started: HMMsearch
[2024-01-24 13:40:43,782] [INFO] Running command: hmmsearch --tblout GCF_002760665.1_ASM276066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5a4a558-d13f-4a04-a364-bf3884913363/dqc_reference/reference_markers.hmm GCF_002760665.1_ASM276066v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:44,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:44,120] [INFO] Found 6/6 markers.
[2024-01-24 13:40:44,163] [INFO] Query marker FASTA was written to GCF_002760665.1_ASM276066v1_genomic.fna/markers.fasta
[2024-01-24 13:40:44,164] [INFO] Task started: Blastn
[2024-01-24 13:40:44,164] [INFO] Running command: blastn -query GCF_002760665.1_ASM276066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5a4a558-d13f-4a04-a364-bf3884913363/dqc_reference/reference_markers.fasta -out GCF_002760665.1_ASM276066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:45,271] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:45,275] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:45,275] [INFO] Target genome list was writen to GCF_002760665.1_ASM276066v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:45,282] [INFO] Task started: fastANI
[2024-01-24 13:40:45,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d1e09c9-cf8f-4062-9330-b5a86f75310c/GCF_002760665.1_ASM276066v1_genomic.fna.gz --refList GCF_002760665.1_ASM276066v1_genomic.fna/target_genomes.txt --output GCF_002760665.1_ASM276066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:06,995] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:06,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5a4a558-d13f-4a04-a364-bf3884913363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:06,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5a4a558-d13f-4a04-a364-bf3884913363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:07,009] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:07,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:07,010] [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
Massilia psychrophila	strain=JCM 30813	GCA_002760665.1	1603353	1603353	type	True	100.0	1527	1530	95	conclusive
Massilia psychrophila	strain=CGMCC 1.15196	GCA_014641415.1	1603353	1603353	type	True	99.9906	1502	1530	95	conclusive
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	85.1001	1087	1530	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	82.32	966	1530	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	82.0383	854	1530	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	82.0372	947	1530	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	82.0223	877	1530	95	below_threshold
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	81.979	859	1530	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	81.9674	920	1530	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	81.9139	940	1530	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.9075	811	1530	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	81.8746	935	1530	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	81.1927	824	1530	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.8795	858	1530	95	below_threshold
Massilia horti	strain=ONC3	GCA_004614195.1	2562153	2562153	type	True	80.8404	768	1530	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	80.7862	825	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:07,012] [INFO] DFAST Taxonomy check result was written to GCF_002760665.1_ASM276066v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:07,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:07,013] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:07,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5a4a558-d13f-4a04-a364-bf3884913363/dqc_reference/checkm_data
[2024-01-24 13:41:07,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:07,064] [INFO] Task started: CheckM
[2024-01-24 13:41:07,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002760665.1_ASM276066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002760665.1_ASM276066v1_genomic.fna/checkm_input GCF_002760665.1_ASM276066v1_genomic.fna/checkm_result
[2024-01-24 13:41:49,787] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:49,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,804] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:49,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:49,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002760665.1_ASM276066v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:49,805] [INFO] Task started: Blastn
[2024-01-24 13:41:49,805] [INFO] Running command: blastn -query GCF_002760665.1_ASM276066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5a4a558-d13f-4a04-a364-bf3884913363/dqc_reference/reference_markers_gtdb.fasta -out GCF_002760665.1_ASM276066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:51,898] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:51,902] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:51,902] [INFO] Target genome list was writen to GCF_002760665.1_ASM276066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:51,910] [INFO] Task started: fastANI
[2024-01-24 13:41:51,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d1e09c9-cf8f-4062-9330-b5a86f75310c/GCF_002760665.1_ASM276066v1_genomic.fna.gz --refList GCF_002760665.1_ASM276066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002760665.1_ASM276066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:07,729] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:07,739] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:07,740] [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_002760665.1	s__Massilia psychrophila	100.0	1527	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_002760655.1	s__Massilia eurypsychrophila	85.1136	1086	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003953935.1	s__Massilia atriviolacea	82.3426	961	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428015.1	s__Massilia sp002428015	82.15	838	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011895.2	s__Massilia glaciei	82.0801	849	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682145.1	s__Massilia mucilaginosa	82.001	951	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752675.1	s__Massilia violaceinigra	81.9657	921	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590855.1	s__Massilia sp003590855	81.9339	808	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682065.1	s__Massilia rubra	81.8927	943	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_011682175.1	s__Massilia frigida	81.8581	939	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682045.1	s__Massilia aquatica	81.8526	941	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	81.5673	461	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:07,741] [INFO] GTDB search result was written to GCF_002760665.1_ASM276066v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:07,742] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:07,745] [INFO] DFAST_QC result json was written to GCF_002760665.1_ASM276066v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:07,746] [INFO] DFAST_QC completed!
[2024-01-24 13:42:07,746] [INFO] Total running time: 0h1m41s