[2024-01-24 11:05:27,667] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg780d43de-b042-45d2-96ee-a80a468eab84/dqc_reference
[2024-01-24 11:05:28,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:28,958] [INFO] Task started: Prodigal
[2024-01-24 11:05:28,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bf379cc-40fa-4366-bfe7-54751d4b61fd/GCF_002973595.1_ASM297359v1_genomic.fna.gz | prodigal -d GCF_002973595.1_ASM297359v1_genomic.fna/cds.fna -a GCF_002973595.1_ASM297359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:42,201] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:42,201] [INFO] Task started: HMMsearch
[2024-01-24 11:05:42,201] [INFO] Running command: hmmsearch --tblout GCF_002973595.1_ASM297359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg780d43de-b042-45d2-96ee-a80a468eab84/dqc_reference/reference_markers.hmm GCF_002973595.1_ASM297359v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:42,524] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:42,526] [INFO] Found 6/6 markers.
[2024-01-24 11:05:42,581] [INFO] Query marker FASTA was written to GCF_002973595.1_ASM297359v1_genomic.fna/markers.fasta
[2024-01-24 11:05:42,581] [INFO] Task started: Blastn
[2024-01-24 11:05:42,581] [INFO] Running command: blastn -query GCF_002973595.1_ASM297359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg780d43de-b042-45d2-96ee-a80a468eab84/dqc_reference/reference_markers.fasta -out GCF_002973595.1_ASM297359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:43,272] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:43,276] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:43,277] [INFO] Target genome list was writen to GCF_002973595.1_ASM297359v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:43,283] [INFO] Task started: fastANI
[2024-01-24 11:05:43,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bf379cc-40fa-4366-bfe7-54751d4b61fd/GCF_002973595.1_ASM297359v1_genomic.fna.gz --refList GCF_002973595.1_ASM297359v1_genomic.fna/target_genomes.txt --output GCF_002973595.1_ASM297359v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:57,193] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:57,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg780d43de-b042-45d2-96ee-a80a468eab84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:57,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg780d43de-b042-45d2-96ee-a80a468eab84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:57,209] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:57,209] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:57,209] [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
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	79.729	624	1351	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	79.402	581	1351	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	79.3646	585	1351	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	79.1773	554	1351	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	78.4812	411	1351	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.3729	432	1351	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.3453	436	1351	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.3032	445	1351	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.798	171	1351	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.7938	360	1351	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7881	361	1351	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.6465	221	1351	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.5866	360	1351	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.5031	302	1351	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	77.4723	285	1351	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.4549	330	1351	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.445	258	1351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:57,211] [INFO] DFAST Taxonomy check result was written to GCF_002973595.1_ASM297359v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:57,212] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:57,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:57,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg780d43de-b042-45d2-96ee-a80a468eab84/dqc_reference/checkm_data
[2024-01-24 11:05:57,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:57,256] [INFO] Task started: CheckM
[2024-01-24 11:05:57,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002973595.1_ASM297359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002973595.1_ASM297359v1_genomic.fna/checkm_input GCF_002973595.1_ASM297359v1_genomic.fna/checkm_result
[2024-01-24 11:06:38,694] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:38,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:38,713] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:38,713] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:38,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002973595.1_ASM297359v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:38,714] [INFO] Task started: Blastn
[2024-01-24 11:06:38,714] [INFO] Running command: blastn -query GCF_002973595.1_ASM297359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg780d43de-b042-45d2-96ee-a80a468eab84/dqc_reference/reference_markers_gtdb.fasta -out GCF_002973595.1_ASM297359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:39,645] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:39,648] [INFO] Selected 12 target genomes.
[2024-01-24 11:06:39,648] [INFO] Target genome list was writen to GCF_002973595.1_ASM297359v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:39,671] [INFO] Task started: fastANI
[2024-01-24 11:06:39,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bf379cc-40fa-4366-bfe7-54751d4b61fd/GCF_002973595.1_ASM297359v1_genomic.fna.gz --refList GCF_002973595.1_ASM297359v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002973595.1_ASM297359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:49,229] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:49,240] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:49,240] [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_002973595.1	s__Jejuia pallidilutea	100.0	1351	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	conclusive
GCF_900111025.1	s__Jejuia jejuensis	80.5606	668	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	79.7249	625	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310335.1	s__Jejuia pacifica	79.4117	581	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016827605.1	s__Jejuia sp016827605	79.1832	554	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428965.1	s__Jejuia sp002428965	78.6472	454	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.5765	448	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	78.4616	413	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.3637	434	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114265.1	s__Flaviramulus basaltis	78.3038	456	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014270105.1	s__Jejuia sp014270105	77.7949	362	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843175.1	s__Confluentibacter flavum	77.4616	286	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:49,242] [INFO] GTDB search result was written to GCF_002973595.1_ASM297359v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:49,242] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:49,247] [INFO] DFAST_QC result json was written to GCF_002973595.1_ASM297359v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:49,248] [INFO] DFAST_QC completed!
[2024-01-24 11:06:49,248] [INFO] Total running time: 0h1m22s