[2023-03-16 17:24:42,808] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:24:42,808] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:24:42,808] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0a4d285-b93a-4291-8796-3f018155996c/dqc_reference
[2023-03-16 17:24:44,011] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:24:44,012] [INFO] Task started: Prodigal
[2023-03-16 17:24:44,012] [INFO] Running command: cat /var/lib/cwl/stg7f9ce8f3-2369-475f-a477-213859d481ad/OceanDNA-b6640.fa | prodigal -d OceanDNA-b6640/cds.fna -a OceanDNA-b6640/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:25:03,849] [INFO] Task succeeded: Prodigal
[2023-03-16 17:25:03,849] [INFO] Task started: HMMsearch
[2023-03-16 17:25:03,849] [INFO] Running command: hmmsearch --tblout OceanDNA-b6640/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0a4d285-b93a-4291-8796-3f018155996c/dqc_reference/reference_markers.hmm OceanDNA-b6640/protein.faa > /dev/null
[2023-03-16 17:25:04,047] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:25:04,047] [INFO] Found 6/6 markers.
[2023-03-16 17:25:04,066] [INFO] Query marker FASTA was written to OceanDNA-b6640/markers.fasta
[2023-03-16 17:25:04,067] [INFO] Task started: Blastn
[2023-03-16 17:25:04,067] [INFO] Running command: blastn -query OceanDNA-b6640/markers.fasta -db /var/lib/cwl/stgb0a4d285-b93a-4291-8796-3f018155996c/dqc_reference/reference_markers.fasta -out OceanDNA-b6640/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:25:04,665] [INFO] Task succeeded: Blastn
[2023-03-16 17:25:04,666] [INFO] Selected 15 target genomes.
[2023-03-16 17:25:04,666] [INFO] Target genome list was writen to OceanDNA-b6640/target_genomes.txt
[2023-03-16 17:25:04,675] [INFO] Task started: fastANI
[2023-03-16 17:25:04,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9ce8f3-2369-475f-a477-213859d481ad/OceanDNA-b6640.fa --refList OceanDNA-b6640/target_genomes.txt --output OceanDNA-b6640/fastani_result.tsv --threads 1
[2023-03-16 17:25:14,336] [INFO] Task succeeded: fastANI
[2023-03-16 17:25:14,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0a4d285-b93a-4291-8796-3f018155996c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:25:14,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0a4d285-b93a-4291-8796-3f018155996c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:25:14,346] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 17:25:14,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 17:25:14,346] [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
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	97.7647	931	1031	95	conclusive
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	84.5005	823	1031	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	80.3973	639	1031	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	80.0505	555	1031	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	78.2086	367	1031	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	78.0159	348	1031	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	78.0021	313	1031	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.84	367	1031	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.5883	305	1031	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.4341	230	1031	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.3136	234	1031	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.2612	252	1031	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.2514	199	1031	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2139	232	1031	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.0334	219	1031	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:25:14,347] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6640/tc_result.tsv
[2023-03-16 17:25:14,347] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:25:14,347] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:25:14,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0a4d285-b93a-4291-8796-3f018155996c/dqc_reference/checkm_data
[2023-03-16 17:25:14,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:25:14,692] [INFO] Task started: CheckM
[2023-03-16 17:25:14,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6640/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6640/checkm_input OceanDNA-b6640/checkm_result
[2023-03-16 17:26:04,999] [INFO] Task succeeded: CheckM
[2023-03-16 17:26:05,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:26:05,002] [INFO] ===== Completeness check finished =====
[2023-03-16 17:26:05,002] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:26:05,002] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6640/markers.fasta)
[2023-03-16 17:26:05,004] [INFO] Task started: Blastn
[2023-03-16 17:26:05,004] [INFO] Running command: blastn -query OceanDNA-b6640/markers.fasta -db /var/lib/cwl/stgb0a4d285-b93a-4291-8796-3f018155996c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6640/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:26:06,020] [INFO] Task succeeded: Blastn
[2023-03-16 17:26:06,021] [INFO] Selected 9 target genomes.
[2023-03-16 17:26:06,021] [INFO] Target genome list was writen to OceanDNA-b6640/target_genomes_gtdb.txt
[2023-03-16 17:26:06,028] [INFO] Task started: fastANI
[2023-03-16 17:26:06,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9ce8f3-2369-475f-a477-213859d481ad/OceanDNA-b6640.fa --refList OceanDNA-b6640/target_genomes_gtdb.txt --output OceanDNA-b6640/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:26:12,925] [INFO] Task succeeded: fastANI
[2023-03-16 17:26:12,931] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:26:12,931] [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_900115185.1	s__Algorimicrobium echini	97.7396	932	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	conclusive
GCF_008086165.1	s__Algorimicrobium algoritergicola	84.5056	823	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002414705.1	s__Algorimicrobium sp002414705	82.8841	739	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086205.1	s__Algorimicrobium myxarmorum	80.388	640	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224335.1	s__Algorimicrobium argentinense	80.0505	555	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895005.1	s__Hanstruepera neustonica	78.0018	313	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hanstruepera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.597	279	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	77.2796	237	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013249065.1	s__Winogradskyella litoriviva	77.2601	253	1031	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:26:12,931] [INFO] GTDB search result was written to OceanDNA-b6640/result_gtdb.tsv
[2023-03-16 17:26:12,931] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:26:12,933] [INFO] DFAST_QC result json was written to OceanDNA-b6640/dqc_result.json
[2023-03-16 17:26:12,933] [INFO] DFAST_QC completed!
[2023-03-16 17:26:12,933] [INFO] Total running time: 0h1m30s