[2024-01-24 15:14:52,467] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:52,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:52,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgca33e6db-9ffd-43c2-9f92-974a1ddc696e/dqc_reference
[2024-01-24 15:14:53,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:53,716] [INFO] Task started: Prodigal
[2024-01-24 15:14:53,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg60fdb3dc-45bf-448d-a0e3-287bdac85541/GCF_003253545.1_ASM325354v1_genomic.fna.gz | prodigal -d GCF_003253545.1_ASM325354v1_genomic.fna/cds.fna -a GCF_003253545.1_ASM325354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:02,904] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:02,904] [INFO] Task started: HMMsearch
[2024-01-24 15:15:02,905] [INFO] Running command: hmmsearch --tblout GCF_003253545.1_ASM325354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca33e6db-9ffd-43c2-9f92-974a1ddc696e/dqc_reference/reference_markers.hmm GCF_003253545.1_ASM325354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:03,182] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:03,184] [INFO] Found 6/6 markers.
[2024-01-24 15:15:03,227] [INFO] Query marker FASTA was written to GCF_003253545.1_ASM325354v1_genomic.fna/markers.fasta
[2024-01-24 15:15:03,227] [INFO] Task started: Blastn
[2024-01-24 15:15:03,227] [INFO] Running command: blastn -query GCF_003253545.1_ASM325354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca33e6db-9ffd-43c2-9f92-974a1ddc696e/dqc_reference/reference_markers.fasta -out GCF_003253545.1_ASM325354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:03,901] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:03,904] [INFO] Selected 22 target genomes.
[2024-01-24 15:15:03,904] [INFO] Target genome list was writen to GCF_003253545.1_ASM325354v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:03,917] [INFO] Task started: fastANI
[2024-01-24 15:15:03,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg60fdb3dc-45bf-448d-a0e3-287bdac85541/GCF_003253545.1_ASM325354v1_genomic.fna.gz --refList GCF_003253545.1_ASM325354v1_genomic.fna/target_genomes.txt --output GCF_003253545.1_ASM325354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:17,151] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:17,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca33e6db-9ffd-43c2-9f92-974a1ddc696e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:17,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca33e6db-9ffd-43c2-9f92-974a1ddc696e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:17,171] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:15:17,171] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:17,171] [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
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	100.0	1011	1013	95	conclusive
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	78.501	364	1013	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	77.9454	305	1013	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	77.8414	311	1013	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	77.5339	279	1013	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	77.2692	233	1013	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.9138	143	1013	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.8192	110	1013	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	76.809	128	1013	95	below_threshold
Salegentibacter salinarum	strain=KCTC 12975	GCA_002833365.1	447422	447422	type	True	76.7875	133	1013	95	below_threshold
Salegentibacter salinarum	strain=DSM 23400	GCA_900168115.1	447422	447422	type	True	76.773	135	1013	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6882	92	1013	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.6822	64	1013	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.6595	97	1013	95	below_threshold
Psychroflexus planctonicus	strain=CGMCC 1.12931	GCA_014640195.1	1526575	1526575	type	True	76.6233	108	1013	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	76.5637	126	1013	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.5609	107	1013	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.5396	123	1013	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.5284	112	1013	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.4558	86	1013	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.3314	107	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:17,173] [INFO] DFAST Taxonomy check result was written to GCF_003253545.1_ASM325354v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:17,173] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:17,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:17,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca33e6db-9ffd-43c2-9f92-974a1ddc696e/dqc_reference/checkm_data
[2024-01-24 15:15:17,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:17,205] [INFO] Task started: CheckM
[2024-01-24 15:15:17,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003253545.1_ASM325354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003253545.1_ASM325354v1_genomic.fna/checkm_input GCF_003253545.1_ASM325354v1_genomic.fna/checkm_result
[2024-01-24 15:15:47,874] [INFO] Task succeeded: CheckM
[2024-01-24 15:15:47,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:15:47,893] [INFO] ===== Completeness check finished =====
[2024-01-24 15:15:47,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:15:47,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003253545.1_ASM325354v1_genomic.fna/markers.fasta)
[2024-01-24 15:15:47,895] [INFO] Task started: Blastn
[2024-01-24 15:15:47,895] [INFO] Running command: blastn -query GCF_003253545.1_ASM325354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca33e6db-9ffd-43c2-9f92-974a1ddc696e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003253545.1_ASM325354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:48,834] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:48,839] [INFO] Selected 16 target genomes.
[2024-01-24 15:15:48,839] [INFO] Target genome list was writen to GCF_003253545.1_ASM325354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:15:48,852] [INFO] Task started: fastANI
[2024-01-24 15:15:48,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg60fdb3dc-45bf-448d-a0e3-287bdac85541/GCF_003253545.1_ASM325354v1_genomic.fna.gz --refList GCF_003253545.1_ASM325354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003253545.1_ASM325354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:15:58,577] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:58,590] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:15:58,590] [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_003253545.1	s__Mesonia algae	100.0	1011	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	conclusive
GCF_900141885.1	s__Mesonia phycicola	78.5124	363	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423405.1	s__Mesonia mobilis	77.8408	311	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003667275.1	s__Mesonia aquimarina	77.7859	312	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017835.1	s__Mesonia sp008017835	77.6652	196	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964435.1	s__Mesonia sp012964435	77.543	282	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_902499555.1	s__Mesonia oceanica	77.5236	280	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCF_008692195.1	s__Mesonia sp008692195	77.2033	292	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233725.1	s__Mesonia sp003233725	77.1663	190	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094855.1	s__Zunongwangia atlantica	76.9138	143	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	76.5702	129	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109375.1	s__Aquimarina amphilecti	76.5637	126	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414705.1	s__Algorimicrobium sp002414705	76.5514	101	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	76.3398	116	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:15:58,592] [INFO] GTDB search result was written to GCF_003253545.1_ASM325354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:15:58,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:15:58,596] [INFO] DFAST_QC result json was written to GCF_003253545.1_ASM325354v1_genomic.fna/dqc_result.json
[2024-01-24 15:15:58,597] [INFO] DFAST_QC completed!
[2024-01-24 15:15:58,597] [INFO] Total running time: 0h1m6s