[2023-03-15 12:44:24,471] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,471] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg963d28ab-ab2f-4a2b-aa28-75e5c3bf952f/dqc_reference
[2023-03-15 12:44:26,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,207] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,208] [INFO] Running command: cat /var/lib/cwl/stg342a32c4-cc7f-49a2-9512-e931298adefc/OceanDNA-b9644.fa | prodigal -d OceanDNA-b9644/cds.fna -a OceanDNA-b9644/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:51,862] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:51,862] [INFO] Task started: HMMsearch
[2023-03-15 12:44:51,862] [INFO] Running command: hmmsearch --tblout OceanDNA-b9644/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg963d28ab-ab2f-4a2b-aa28-75e5c3bf952f/dqc_reference/reference_markers.hmm OceanDNA-b9644/protein.faa > /dev/null
[2023-03-15 12:44:52,117] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:52,118] [INFO] Found 6/6 markers.
[2023-03-15 12:44:52,145] [INFO] Query marker FASTA was written to OceanDNA-b9644/markers.fasta
[2023-03-15 12:44:52,145] [INFO] Task started: Blastn
[2023-03-15 12:44:52,145] [INFO] Running command: blastn -query OceanDNA-b9644/markers.fasta -db /var/lib/cwl/stg963d28ab-ab2f-4a2b-aa28-75e5c3bf952f/dqc_reference/reference_markers.fasta -out OceanDNA-b9644/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:52,767] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:52,768] [INFO] Selected 15 target genomes.
[2023-03-15 12:44:52,768] [INFO] Target genome list was writen to OceanDNA-b9644/target_genomes.txt
[2023-03-15 12:44:52,777] [INFO] Task started: fastANI
[2023-03-15 12:44:52,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg342a32c4-cc7f-49a2-9512-e931298adefc/OceanDNA-b9644.fa --refList OceanDNA-b9644/target_genomes.txt --output OceanDNA-b9644/fastani_result.tsv --threads 1
[2023-03-15 12:45:03,982] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:03,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg963d28ab-ab2f-4a2b-aa28-75e5c3bf952f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:45:03,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg963d28ab-ab2f-4a2b-aa28-75e5c3bf952f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:45:03,991] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:45:03,991] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:45:03,991] [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
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	92.8022	1079	1276	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	89.0239	1017	1276	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	80.2003	675	1276	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	80.1853	675	1276	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	80.1782	658	1276	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	79.9646	675	1276	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	79.8291	654	1276	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	79.7833	589	1276	95	below_threshold
Maribacter antarcticus	strain=DSM 21422	GCA_000621125.1	505250	505250	type	True	77.1194	195	1276	95	below_threshold
Aurantibacter crassamenti	strain=HG732	GCA_016811105.1	1837375	1837375	type	True	76.6329	194	1276	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.0735	90	1276	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	75.9934	78	1276	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.9365	74	1276	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:45:03,991] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9644/tc_result.tsv
[2023-03-15 12:45:03,991] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:45:03,992] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:45:03,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg963d28ab-ab2f-4a2b-aa28-75e5c3bf952f/dqc_reference/checkm_data
[2023-03-15 12:45:03,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:45:04,038] [INFO] Task started: CheckM
[2023-03-15 12:45:04,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9644/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9644/checkm_input OceanDNA-b9644/checkm_result
[2023-03-15 12:46:07,000] [INFO] Task succeeded: CheckM
[2023-03-15 12:46:07,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.22%
Contamintation: 6.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 12:46:07,004] [INFO] ===== Completeness check finished =====
[2023-03-15 12:46:07,004] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:46:07,004] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9644/markers.fasta)
[2023-03-15 12:46:07,005] [INFO] Task started: Blastn
[2023-03-15 12:46:07,005] [INFO] Running command: blastn -query OceanDNA-b9644/markers.fasta -db /var/lib/cwl/stg963d28ab-ab2f-4a2b-aa28-75e5c3bf952f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9644/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:46:07,884] [INFO] Task succeeded: Blastn
[2023-03-15 12:46:07,885] [INFO] Selected 12 target genomes.
[2023-03-15 12:46:07,885] [INFO] Target genome list was writen to OceanDNA-b9644/target_genomes_gtdb.txt
[2023-03-15 12:46:07,907] [INFO] Task started: fastANI
[2023-03-15 12:46:07,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg342a32c4-cc7f-49a2-9512-e931298adefc/OceanDNA-b9644.fa --refList OceanDNA-b9644/target_genomes_gtdb.txt --output OceanDNA-b9644/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:46:18,293] [INFO] Task succeeded: fastANI
[2023-03-15 12:46:18,302] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:46:18,302] [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_900109345.1	s__Maribacter orientalis	92.8012	1079	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	89.0456	1015	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	80.2099	681	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900112245.1	s__Maribacter stanieri	80.1924	676	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_005771495.1	s__Maribacter sp005771495	80.1859	714	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	80.177	675	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142175.1	s__Maribacter aquivivus	79.9771	672	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	79.8543	640	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	79.8208	655	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	79.7861	587	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621125.1	s__Maribacter antarcticus	77.1177	196	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811105.1	s__Aurantibacter_A crassamenti	76.63	193	1276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:46:18,302] [INFO] GTDB search result was written to OceanDNA-b9644/result_gtdb.tsv
[2023-03-15 12:46:18,303] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:46:18,305] [INFO] DFAST_QC result json was written to OceanDNA-b9644/dqc_result.json
[2023-03-15 12:46:18,305] [INFO] DFAST_QC completed!
[2023-03-15 12:46:18,305] [INFO] Total running time: 0h1m54s