[2024-01-25 19:11:50,764] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:50,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:50,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg0df40424-5efa-427c-9402-b563771b14bb/dqc_reference
[2024-01-25 19:11:51,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:51,895] [INFO] Task started: Prodigal
[2024-01-25 19:11:51,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d34c0ff-0e09-4f0d-b797-bd1418a4ad18/GCF_016924145.1_ASM1692414v1_genomic.fna.gz | prodigal -d GCF_016924145.1_ASM1692414v1_genomic.fna/cds.fna -a GCF_016924145.1_ASM1692414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:01,767] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:01,768] [INFO] Task started: HMMsearch
[2024-01-25 19:12:01,768] [INFO] Running command: hmmsearch --tblout GCF_016924145.1_ASM1692414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0df40424-5efa-427c-9402-b563771b14bb/dqc_reference/reference_markers.hmm GCF_016924145.1_ASM1692414v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:02,047] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:02,048] [INFO] Found 6/6 markers.
[2024-01-25 19:12:02,086] [INFO] Query marker FASTA was written to GCF_016924145.1_ASM1692414v1_genomic.fna/markers.fasta
[2024-01-25 19:12:02,086] [INFO] Task started: Blastn
[2024-01-25 19:12:02,086] [INFO] Running command: blastn -query GCF_016924145.1_ASM1692414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0df40424-5efa-427c-9402-b563771b14bb/dqc_reference/reference_markers.fasta -out GCF_016924145.1_ASM1692414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:02,679] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:02,682] [INFO] Selected 18 target genomes.
[2024-01-25 19:12:02,682] [INFO] Target genome list was writen to GCF_016924145.1_ASM1692414v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:02,688] [INFO] Task started: fastANI
[2024-01-25 19:12:02,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d34c0ff-0e09-4f0d-b797-bd1418a4ad18/GCF_016924145.1_ASM1692414v1_genomic.fna.gz --refList GCF_016924145.1_ASM1692414v1_genomic.fna/target_genomes.txt --output GCF_016924145.1_ASM1692414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:17,209] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:17,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0df40424-5efa-427c-9402-b563771b14bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:17,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0df40424-5efa-427c-9402-b563771b14bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:17,218] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:12:17,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:17,219] [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
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	100.0	1499	1504	95	conclusive
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	94.1172	1319	1504	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	79.7708	544	1504	95	below_threshold
Amphritea japonica	strain=JAMM 1866	GCA_000381785.1	452627	452627	type	True	79.1033	531	1504	95	below_threshold
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	79.0893	533	1504	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	79.0405	539	1504	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	78.816	414	1504	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	78.7563	412	1504	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	78.3148	171	1504	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	78.2467	238	1504	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	76.9366	126	1504	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.7701	160	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:17,220] [INFO] DFAST Taxonomy check result was written to GCF_016924145.1_ASM1692414v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:17,220] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:17,220] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:17,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0df40424-5efa-427c-9402-b563771b14bb/dqc_reference/checkm_data
[2024-01-25 19:12:17,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:17,267] [INFO] Task started: CheckM
[2024-01-25 19:12:17,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016924145.1_ASM1692414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016924145.1_ASM1692414v1_genomic.fna/checkm_input GCF_016924145.1_ASM1692414v1_genomic.fna/checkm_result
[2024-01-25 19:12:49,833] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:49,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:49,854] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:49,854] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:49,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016924145.1_ASM1692414v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:49,855] [INFO] Task started: Blastn
[2024-01-25 19:12:49,855] [INFO] Running command: blastn -query GCF_016924145.1_ASM1692414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0df40424-5efa-427c-9402-b563771b14bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016924145.1_ASM1692414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:50,716] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:50,720] [INFO] Selected 8 target genomes.
[2024-01-25 19:12:50,721] [INFO] Target genome list was writen to GCF_016924145.1_ASM1692414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:50,727] [INFO] Task started: fastANI
[2024-01-25 19:12:50,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d34c0ff-0e09-4f0d-b797-bd1418a4ad18/GCF_016924145.1_ASM1692414v1_genomic.fna.gz --refList GCF_016924145.1_ASM1692414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016924145.1_ASM1692414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:59,084] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:59,090] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:59,091] [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_016924235.1	s__Amphritea sp016924235	99.2464	1420	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	conclusive
GCF_900111095.1	s__Amphritea atlantica	94.1023	1320	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223185.1	s__Amphritea sp018223185	83.4718	1016	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCF_003957515.1	s__Amphritea opalescens	79.7896	542	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860855.1	s__Amphritea atlantica_A	79.6606	567	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592435.1	s__Amphritea japonica	79.0322	540	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003858655.1	s__Amphritea balenae	78.8289	412	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017051665.1	s__Amphritea spongicola	78.2659	235	1504	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:59,093] [INFO] GTDB search result was written to GCF_016924145.1_ASM1692414v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:59,093] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:59,096] [INFO] DFAST_QC result json was written to GCF_016924145.1_ASM1692414v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:59,096] [INFO] DFAST_QC completed!
[2024-01-25 19:12:59,096] [INFO] Total running time: 0h1m8s