[2024-01-24 12:06:33,533] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,535] [INFO] DQC Reference Directory: /var/lib/cwl/stgc227c4d1-8b44-4a89-ae13-614cef484ede/dqc_reference
[2024-01-24 12:06:34,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,820] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,821] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7749289-0395-4632-b329-a1f47e266166/GCF_022669015.1_ASM2266901v1_genomic.fna.gz | prodigal -d GCF_022669015.1_ASM2266901v1_genomic.fna/cds.fna -a GCF_022669015.1_ASM2266901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:45,292] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:45,293] [INFO] Task started: HMMsearch
[2024-01-24 12:06:45,293] [INFO] Running command: hmmsearch --tblout GCF_022669015.1_ASM2266901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc227c4d1-8b44-4a89-ae13-614cef484ede/dqc_reference/reference_markers.hmm GCF_022669015.1_ASM2266901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:45,618] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:45,619] [INFO] Found 6/6 markers.
[2024-01-24 12:06:45,675] [INFO] Query marker FASTA was written to GCF_022669015.1_ASM2266901v1_genomic.fna/markers.fasta
[2024-01-24 12:06:45,676] [INFO] Task started: Blastn
[2024-01-24 12:06:45,676] [INFO] Running command: blastn -query GCF_022669015.1_ASM2266901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc227c4d1-8b44-4a89-ae13-614cef484ede/dqc_reference/reference_markers.fasta -out GCF_022669015.1_ASM2266901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:46,379] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:46,384] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:46,385] [INFO] Target genome list was writen to GCF_022669015.1_ASM2266901v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:46,395] [INFO] Task started: fastANI
[2024-01-24 12:06:46,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7749289-0395-4632-b329-a1f47e266166/GCF_022669015.1_ASM2266901v1_genomic.fna.gz --refList GCF_022669015.1_ASM2266901v1_genomic.fna/target_genomes.txt --output GCF_022669015.1_ASM2266901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:57,361] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:57,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc227c4d1-8b44-4a89-ae13-614cef484ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:57,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc227c4d1-8b44-4a89-ae13-614cef484ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:57,375] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:57,375] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:57,375] [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
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.9716	307	1739	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.8149	310	1739	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.6546	346	1739	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.609	303	1739	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.438	297	1739	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.4324	273	1739	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.3817	301	1739	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.3346	297	1739	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.2556	162	1739	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	75.7451	53	1739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:57,377] [INFO] DFAST Taxonomy check result was written to GCF_022669015.1_ASM2266901v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:57,378] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:57,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:57,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc227c4d1-8b44-4a89-ae13-614cef484ede/dqc_reference/checkm_data
[2024-01-24 12:06:57,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:57,428] [INFO] Task started: CheckM
[2024-01-24 12:06:57,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022669015.1_ASM2266901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022669015.1_ASM2266901v1_genomic.fna/checkm_input GCF_022669015.1_ASM2266901v1_genomic.fna/checkm_result
[2024-01-24 12:07:32,228] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:32,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:32,253] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:32,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:32,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022669015.1_ASM2266901v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:32,255] [INFO] Task started: Blastn
[2024-01-24 12:07:32,255] [INFO] Running command: blastn -query GCF_022669015.1_ASM2266901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc227c4d1-8b44-4a89-ae13-614cef484ede/dqc_reference/reference_markers_gtdb.fasta -out GCF_022669015.1_ASM2266901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:33,345] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:33,350] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:33,350] [INFO] Target genome list was writen to GCF_022669015.1_ASM2266901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:33,359] [INFO] Task started: fastANI
[2024-01-24 12:07:33,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7749289-0395-4632-b329-a1f47e266166/GCF_022669015.1_ASM2266901v1_genomic.fna.gz --refList GCF_022669015.1_ASM2266901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022669015.1_ASM2266901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:43,799] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:43,816] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:07:43,816] [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
GCA_016745015.1	s__Colwellia sp016745015	80.0889	499	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	80.0886	607	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860915.1	s__Colwellia sp018860915	79.5633	566	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162675.1	s__Colwellia sp002162675	79.5619	424	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215465.1	s__Colwellia sp013215465	79.0211	474	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_003333305.1	s__Colwellia aromaticivorans	79.0128	459	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	78.9805	442	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_003521815.1	s__Colwellia sp003521815	78.7986	322	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	78.7983	310	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860755.1	s__Colwellia sp018860755	78.7068	301	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843355.2	s__Colwellia echini	78.597	304	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765685.1	s__Colwellia sp016765685	78.4848	336	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378625.1	s__Colwellia piezophila	78.4408	296	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	78.1383	291	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:43,818] [INFO] GTDB search result was written to GCF_022669015.1_ASM2266901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:43,818] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:43,822] [INFO] DFAST_QC result json was written to GCF_022669015.1_ASM2266901v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:43,822] [INFO] DFAST_QC completed!
[2024-01-24 12:07:43,822] [INFO] Total running time: 0h1m10s