[2024-01-25 18:44:50,591] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:50,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:50,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg57d244d4-ce8b-471a-9197-4081acd4339a/dqc_reference
[2024-01-25 18:44:51,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:51,686] [INFO] Task started: Prodigal
[2024-01-25 18:44:51,686] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3cf4587-2a70-4675-9fbd-12f90d1d8745/GCF_002283365.1_ASM228336v1_genomic.fna.gz | prodigal -d GCF_002283365.1_ASM228336v1_genomic.fna/cds.fna -a GCF_002283365.1_ASM228336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:11,437] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:11,437] [INFO] Task started: HMMsearch
[2024-01-25 18:45:11,437] [INFO] Running command: hmmsearch --tblout GCF_002283365.1_ASM228336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57d244d4-ce8b-471a-9197-4081acd4339a/dqc_reference/reference_markers.hmm GCF_002283365.1_ASM228336v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:11,719] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:11,720] [INFO] Found 6/6 markers.
[2024-01-25 18:45:11,761] [INFO] Query marker FASTA was written to GCF_002283365.1_ASM228336v1_genomic.fna/markers.fasta
[2024-01-25 18:45:11,761] [INFO] Task started: Blastn
[2024-01-25 18:45:11,761] [INFO] Running command: blastn -query GCF_002283365.1_ASM228336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57d244d4-ce8b-471a-9197-4081acd4339a/dqc_reference/reference_markers.fasta -out GCF_002283365.1_ASM228336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:12,417] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:12,421] [INFO] Selected 20 target genomes.
[2024-01-25 18:45:12,421] [INFO] Target genome list was writen to GCF_002283365.1_ASM228336v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:12,450] [INFO] Task started: fastANI
[2024-01-25 18:45:12,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3cf4587-2a70-4675-9fbd-12f90d1d8745/GCF_002283365.1_ASM228336v1_genomic.fna.gz --refList GCF_002283365.1_ASM228336v1_genomic.fna/target_genomes.txt --output GCF_002283365.1_ASM228336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:31,443] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:31,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57d244d4-ce8b-471a-9197-4081acd4339a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:31,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57d244d4-ce8b-471a-9197-4081acd4339a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:31,455] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:45:31,455] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:31,455] [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
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	100.0	1657	1657	95	conclusive
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	78.0717	576	1657	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.4296	259	1657	95	below_threshold
Salinibacter altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	75.6114	98	1657	95	below_threshold
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	75.5928	145	1657	95	below_threshold
Longibacter salinarum	strain=KCTC 52045	GCA_002554795.1	1850348	1850348	type	True	75.5042	68	1657	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	74.8985	110	1657	95	below_threshold
Roseitranquillus sediminis	strain=MCCB 386	GCA_016918935.1	2809051	2809051	type	True	74.8926	112	1657	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	74.8621	404	1657	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	74.8551	99	1657	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	74.8435	206	1657	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.8155	319	1657	95	below_threshold
Williamsia herbipolensis	strain=ARP1	GCA_000964005.1	1603258	1603258	type	True	74.8135	137	1657	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	74.8035	419	1657	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	74.8004	245	1657	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	74.7925	391	1657	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	74.7764	238	1657	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	74.7703	401	1657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:31,458] [INFO] DFAST Taxonomy check result was written to GCF_002283365.1_ASM228336v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:31,460] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:31,460] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:31,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57d244d4-ce8b-471a-9197-4081acd4339a/dqc_reference/checkm_data
[2024-01-25 18:45:31,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:31,509] [INFO] Task started: CheckM
[2024-01-25 18:45:31,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002283365.1_ASM228336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002283365.1_ASM228336v1_genomic.fna/checkm_input GCF_002283365.1_ASM228336v1_genomic.fna/checkm_result
[2024-01-25 18:46:24,610] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:24,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:24,631] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:24,631] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:24,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002283365.1_ASM228336v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:24,632] [INFO] Task started: Blastn
[2024-01-25 18:46:24,632] [INFO] Running command: blastn -query GCF_002283365.1_ASM228336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57d244d4-ce8b-471a-9197-4081acd4339a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002283365.1_ASM228336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:25,646] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:25,649] [INFO] Selected 6 target genomes.
[2024-01-25 18:46:25,649] [INFO] Target genome list was writen to GCF_002283365.1_ASM228336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:25,653] [INFO] Task started: fastANI
[2024-01-25 18:46:25,653] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3cf4587-2a70-4675-9fbd-12f90d1d8745/GCF_002283365.1_ASM228336v1_genomic.fna.gz --refList GCF_002283365.1_ASM228336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002283365.1_ASM228336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:32,270] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:32,276] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:32,276] [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_002283365.1	s__Rubrivirga marina	100.0	1657	1657	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012269805.1	s__Rubrivirga sp012269805	88.9756	770	1657	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	82.1427	1011	1657	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCA_012960515.1	s__Rubricoccus sp012960515	79.0067	588	1657	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	78.0703	577	1657	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003465.1	s__JABDIZ01 sp013003465	77.6901	286	1657	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:32,277] [INFO] GTDB search result was written to GCF_002283365.1_ASM228336v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:32,278] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:32,280] [INFO] DFAST_QC result json was written to GCF_002283365.1_ASM228336v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:32,281] [INFO] DFAST_QC completed!
[2024-01-25 18:46:32,281] [INFO] Total running time: 0h1m42s