[2024-01-24 11:48:21,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg43dd217e-d3ab-49ce-9263-caede51caf2f/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,567] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d414724-959a-48ef-a27a-4e213d4caceb/GCF_014651495.1_ASM1465149v1_genomic.fna.gz | prodigal -d GCF_014651495.1_ASM1465149v1_genomic.fna/cds.fna -a GCF_014651495.1_ASM1465149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:39,102] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:39,103] [INFO] Task started: HMMsearch
[2024-01-24 11:48:39,103] [INFO] Running command: hmmsearch --tblout GCF_014651495.1_ASM1465149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43dd217e-d3ab-49ce-9263-caede51caf2f/dqc_reference/reference_markers.hmm GCF_014651495.1_ASM1465149v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:39,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:39,384] [INFO] Found 6/6 markers.
[2024-01-24 11:48:39,422] [INFO] Query marker FASTA was written to GCF_014651495.1_ASM1465149v1_genomic.fna/markers.fasta
[2024-01-24 11:48:39,422] [INFO] Task started: Blastn
[2024-01-24 11:48:39,422] [INFO] Running command: blastn -query GCF_014651495.1_ASM1465149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43dd217e-d3ab-49ce-9263-caede51caf2f/dqc_reference/reference_markers.fasta -out GCF_014651495.1_ASM1465149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:40,093] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:40,097] [INFO] Selected 21 target genomes.
[2024-01-24 11:48:40,098] [INFO] Target genome list was writen to GCF_014651495.1_ASM1465149v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:40,106] [INFO] Task started: fastANI
[2024-01-24 11:48:40,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d414724-959a-48ef-a27a-4e213d4caceb/GCF_014651495.1_ASM1465149v1_genomic.fna.gz --refList GCF_014651495.1_ASM1465149v1_genomic.fna/target_genomes.txt --output GCF_014651495.1_ASM1465149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:54,723] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:54,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43dd217e-d3ab-49ce-9263-caede51caf2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:54,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43dd217e-d3ab-49ce-9263-caede51caf2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:54,747] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:48:54,747] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:48:54,748] [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
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	100.0	1459	1460	95	conclusive
Algibacter onchidii	strain=XY-114	GCA_004804355.1	2562860	2562860	type	True	79.4246	515	1460	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	79.1213	433	1460	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.5891	402	1460	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.5796	403	1460	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.5501	403	1460	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.5346	322	1460	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.415	385	1460	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	78.3158	328	1460	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.1058	325	1460	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.0831	357	1460	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.073	379	1460	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	78.0314	335	1460	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.9912	377	1460	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.8043	292	1460	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.6263	276	1460	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.6194	265	1460	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	77.6069	295	1460	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	77.5049	270	1460	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.49	192	1460	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.3367	139	1460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:54,749] [INFO] DFAST Taxonomy check result was written to GCF_014651495.1_ASM1465149v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:54,750] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:54,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:54,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43dd217e-d3ab-49ce-9263-caede51caf2f/dqc_reference/checkm_data
[2024-01-24 11:48:54,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:54,798] [INFO] Task started: CheckM
[2024-01-24 11:48:54,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651495.1_ASM1465149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651495.1_ASM1465149v1_genomic.fna/checkm_input GCF_014651495.1_ASM1465149v1_genomic.fna/checkm_result
[2024-01-24 11:49:39,043] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:39,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:39,064] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:39,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:39,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651495.1_ASM1465149v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:39,065] [INFO] Task started: Blastn
[2024-01-24 11:49:39,066] [INFO] Running command: blastn -query GCF_014651495.1_ASM1465149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43dd217e-d3ab-49ce-9263-caede51caf2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651495.1_ASM1465149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:40,017] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:40,022] [INFO] Selected 19 target genomes.
[2024-01-24 11:49:40,023] [INFO] Target genome list was writen to GCF_014651495.1_ASM1465149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:40,038] [INFO] Task started: fastANI
[2024-01-24 11:49:40,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d414724-959a-48ef-a27a-4e213d4caceb/GCF_014651495.1_ASM1465149v1_genomic.fna.gz --refList GCF_014651495.1_ASM1465149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651495.1_ASM1465149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:49:53,208] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:53,230] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:49:53,230] [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_014651495.1	s__Algibacter_E mikhailovii	100.0	1459	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004804355.1	s__Tamlana_C sp004804355	79.4203	514	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	79.1022	436	1460	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_018860245.1	s__Tamlana_A agarivorans_A	78.6697	347	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.6617	385	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.6123	363	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.56	402	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900114265.1	s__Flaviramulus basaltis	78.5058	430	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.4528	403	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	78.4382	293	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	78.4301	383	1460	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_006265225.1	s__Tamlana_C fucoidanivorans	78.3205	410	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	78.1989	359	1460	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_004791695.1	s__Flavivirga rizhaonensis	78.0636	380	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	78.0314	335	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	78.0159	375	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	77.5332	304	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386195.1	s__Seonamhaeicola aphaedonensis	77.494	271	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	77.4219	205	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:49:53,232] [INFO] GTDB search result was written to GCF_014651495.1_ASM1465149v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:49:53,232] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:49:53,237] [INFO] DFAST_QC result json was written to GCF_014651495.1_ASM1465149v1_genomic.fna/dqc_result.json
[2024-01-24 11:49:53,237] [INFO] DFAST_QC completed!
[2024-01-24 11:49:53,237] [INFO] Total running time: 0h1m32s