[2024-01-24 12:06:14,265] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg48dc4389-8b4b-453f-ac48-a29f094d63a0/dqc_reference
[2024-01-24 12:06:15,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,578] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,579] [INFO] Running command: gunzip -c /var/lib/cwl/stg2950ef4f-7335-4574-8e8b-4ee52eec0d16/GCF_002895005.1_ASM289500v1_genomic.fna.gz | prodigal -d GCF_002895005.1_ASM289500v1_genomic.fna/cds.fna -a GCF_002895005.1_ASM289500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:27,863] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:27,863] [INFO] Task started: HMMsearch
[2024-01-24 12:06:27,863] [INFO] Running command: hmmsearch --tblout GCF_002895005.1_ASM289500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48dc4389-8b4b-453f-ac48-a29f094d63a0/dqc_reference/reference_markers.hmm GCF_002895005.1_ASM289500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:28,227] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:28,229] [INFO] Found 6/6 markers.
[2024-01-24 12:06:28,288] [INFO] Query marker FASTA was written to GCF_002895005.1_ASM289500v1_genomic.fna/markers.fasta
[2024-01-24 12:06:28,288] [INFO] Task started: Blastn
[2024-01-24 12:06:28,288] [INFO] Running command: blastn -query GCF_002895005.1_ASM289500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48dc4389-8b4b-453f-ac48-a29f094d63a0/dqc_reference/reference_markers.fasta -out GCF_002895005.1_ASM289500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:29,027] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:29,030] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:29,030] [INFO] Target genome list was writen to GCF_002895005.1_ASM289500v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:29,037] [INFO] Task started: fastANI
[2024-01-24 12:06:29,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg2950ef4f-7335-4574-8e8b-4ee52eec0d16/GCF_002895005.1_ASM289500v1_genomic.fna.gz --refList GCF_002895005.1_ASM289500v1_genomic.fna/target_genomes.txt --output GCF_002895005.1_ASM289500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:40,266] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:40,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48dc4389-8b4b-453f-ac48-a29f094d63a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:40,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48dc4389-8b4b-453f-ac48-a29f094d63a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:40,280] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:40,281] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:40,281] [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
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	100.0	1005	1008	95	conclusive
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	80.6418	525	1008	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	80.3386	532	1008	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	80.0768	608	1008	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	78.0187	260	1008	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	77.876	174	1008	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.8706	319	1008	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.7582	265	1008	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.757	187	1008	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	77.4298	150	1008	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.4274	197	1008	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.3865	193	1008	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.3211	218	1008	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.2876	168	1008	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.2551	197	1008	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	77.1023	157	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:40,287] [INFO] DFAST Taxonomy check result was written to GCF_002895005.1_ASM289500v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:40,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:40,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:40,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48dc4389-8b4b-453f-ac48-a29f094d63a0/dqc_reference/checkm_data
[2024-01-24 12:06:40,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:40,347] [INFO] Task started: CheckM
[2024-01-24 12:06:40,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002895005.1_ASM289500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002895005.1_ASM289500v1_genomic.fna/checkm_input GCF_002895005.1_ASM289500v1_genomic.fna/checkm_result
[2024-01-24 12:07:20,266] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:20,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:20,293] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:20,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:20,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002895005.1_ASM289500v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:20,295] [INFO] Task started: Blastn
[2024-01-24 12:07:20,295] [INFO] Running command: blastn -query GCF_002895005.1_ASM289500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48dc4389-8b4b-453f-ac48-a29f094d63a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002895005.1_ASM289500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:21,346] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:21,349] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:21,350] [INFO] Target genome list was writen to GCF_002895005.1_ASM289500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:21,375] [INFO] Task started: fastANI
[2024-01-24 12:07:21,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg2950ef4f-7335-4574-8e8b-4ee52eec0d16/GCF_002895005.1_ASM289500v1_genomic.fna.gz --refList GCF_002895005.1_ASM289500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002895005.1_ASM289500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:31,380] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:31,412] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:31,413] [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_002895005.1	s__Hanstruepera neustonica	100.0	1005	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hanstruepera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012931685.1	s__Pseudobizionia ponticola	80.0725	608	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCF_004366715.1	s__Meridianimaribacter flavus	78.4431	261	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_900115185.1	s__Algorimicrobium echini	78.0807	317	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCF_008086205.1	s__Algorimicrobium myxarmorum	78.014	261	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414705.1	s__Algorimicrobium sp002414705	77.9722	314	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	77.9188	290	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	77.8706	319	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000348685.1	s__Xanthomarina gelatinilytica	77.7555	266	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	98.37	98.31	0.90	0.88	4	-
GCF_003663945.1	s__Lacinutrix venerupis	77.634	176	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.6101	226	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826645.1	s__Psychroserpens mesophilus	77.3187	219	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	77.2951	169	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	77.2551	197	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426755.1	s__Aquaticitalea sp002426755	77.0662	155	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280395.1	s__Confluentibacter sp002280395	77.0069	111	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	76.9858	193	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:31,415] [INFO] GTDB search result was written to GCF_002895005.1_ASM289500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:31,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:31,421] [INFO] DFAST_QC result json was written to GCF_002895005.1_ASM289500v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:31,421] [INFO] DFAST_QC completed!
[2024-01-24 12:07:31,421] [INFO] Total running time: 0h1m17s