[2024-01-24 13:49:00,287] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,290] [INFO] DQC Reference Directory: /var/lib/cwl/stgd38b3ad8-6e8a-41c3-b126-0868c0fbba87/dqc_reference
[2024-01-24 13:49:01,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,606] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg8aa017cf-47bd-4fd0-a67c-df5ab374bd2a/GCF_000155675.2_ASM15567v2_genomic.fna.gz | prodigal -d GCF_000155675.2_ASM15567v2_genomic.fna/cds.fna -a GCF_000155675.2_ASM15567v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:17,552] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:17,553] [INFO] Task started: HMMsearch
[2024-01-24 13:49:17,553] [INFO] Running command: hmmsearch --tblout GCF_000155675.2_ASM15567v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd38b3ad8-6e8a-41c3-b126-0868c0fbba87/dqc_reference/reference_markers.hmm GCF_000155675.2_ASM15567v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:17,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:17,841] [INFO] Found 6/6 markers.
[2024-01-24 13:49:17,884] [INFO] Query marker FASTA was written to GCF_000155675.2_ASM15567v2_genomic.fna/markers.fasta
[2024-01-24 13:49:17,884] [INFO] Task started: Blastn
[2024-01-24 13:49:17,884] [INFO] Running command: blastn -query GCF_000155675.2_ASM15567v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd38b3ad8-6e8a-41c3-b126-0868c0fbba87/dqc_reference/reference_markers.fasta -out GCF_000155675.2_ASM15567v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:18,560] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:18,564] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:18,565] [INFO] Target genome list was writen to GCF_000155675.2_ASM15567v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:18,587] [INFO] Task started: fastANI
[2024-01-24 13:49:18,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aa017cf-47bd-4fd0-a67c-df5ab374bd2a/GCF_000155675.2_ASM15567v2_genomic.fna.gz --refList GCF_000155675.2_ASM15567v2_genomic.fna/target_genomes.txt --output GCF_000155675.2_ASM15567v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:28,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:28,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd38b3ad8-6e8a-41c3-b126-0868c0fbba87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:28,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd38b3ad8-6e8a-41c3-b126-0868c0fbba87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:28,975] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:28,975] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:28,976] [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
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	100.0	1623	1624	95	conclusive
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	84.2466	986	1624	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	78.3882	446	1624	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	78.3286	437	1624	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	78.3219	436	1624	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.3125	311	1624	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.8474	109	1624	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.402	117	1624	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.2568	98	1624	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.1032	121	1624	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.8659	72	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:28,977] [INFO] DFAST Taxonomy check result was written to GCF_000155675.2_ASM15567v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:28,978] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:28,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:28,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd38b3ad8-6e8a-41c3-b126-0868c0fbba87/dqc_reference/checkm_data
[2024-01-24 13:49:28,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:29,030] [INFO] Task started: CheckM
[2024-01-24 13:49:29,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000155675.2_ASM15567v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000155675.2_ASM15567v2_genomic.fna/checkm_input GCF_000155675.2_ASM15567v2_genomic.fna/checkm_result
[2024-01-24 13:50:17,512] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:17,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,535] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:17,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:17,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000155675.2_ASM15567v2_genomic.fna/markers.fasta)
[2024-01-24 13:50:17,536] [INFO] Task started: Blastn
[2024-01-24 13:50:17,537] [INFO] Running command: blastn -query GCF_000155675.2_ASM15567v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd38b3ad8-6e8a-41c3-b126-0868c0fbba87/dqc_reference/reference_markers_gtdb.fasta -out GCF_000155675.2_ASM15567v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:18,471] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:18,475] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:18,475] [INFO] Target genome list was writen to GCF_000155675.2_ASM15567v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:18,505] [INFO] Task started: fastANI
[2024-01-24 13:50:18,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aa017cf-47bd-4fd0-a67c-df5ab374bd2a/GCF_000155675.2_ASM15567v2_genomic.fna.gz --refList GCF_000155675.2_ASM15567v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000155675.2_ASM15567v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:27,351] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:27,359] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:27,359] [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_000155675.2	s__Octadecabacter antarcticus	100.0	1622	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017886375.1	s__Octadecabacter sp017886375	84.9139	759	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155735.2	s__Octadecabacter arcticus	84.2739	983	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCA_018500005.1	s__Octadecabacter sp018500005	78.673	324	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608045.1	s__Octadecabacter sp018608045	78.5898	409	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	78.3707	448	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	78.3286	437	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018861045.1	s__Octadecabacter sp018861045	77.8136	384	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:27,361] [INFO] GTDB search result was written to GCF_000155675.2_ASM15567v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:27,362] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:27,365] [INFO] DFAST_QC result json was written to GCF_000155675.2_ASM15567v2_genomic.fna/dqc_result.json
[2024-01-24 13:50:27,366] [INFO] DFAST_QC completed!
[2024-01-24 13:50:27,366] [INFO] Total running time: 0h1m27s