[2023-03-16 03:47:34,626] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:34,627] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:34,627] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4017d00-0c69-4902-9866-5eb3ad8364b8/dqc_reference
[2023-03-16 03:47:35,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:35,728] [INFO] Task started: Prodigal
[2023-03-16 03:47:35,728] [INFO] Running command: cat /var/lib/cwl/stg2c90d075-4898-4402-a549-5f70cf70ffb3/OceanDNA-b30624.fa | prodigal -d OceanDNA-b30624/cds.fna -a OceanDNA-b30624/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:55,605] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:55,605] [INFO] Task started: HMMsearch
[2023-03-16 03:47:55,605] [INFO] Running command: hmmsearch --tblout OceanDNA-b30624/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4017d00-0c69-4902-9866-5eb3ad8364b8/dqc_reference/reference_markers.hmm OceanDNA-b30624/protein.faa > /dev/null
[2023-03-16 03:47:55,844] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:55,845] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2c90d075-4898-4402-a549-5f70cf70ffb3/OceanDNA-b30624.fa]
[2023-03-16 03:47:55,866] [INFO] Query marker FASTA was written to OceanDNA-b30624/markers.fasta
[2023-03-16 03:47:55,866] [INFO] Task started: Blastn
[2023-03-16 03:47:55,866] [INFO] Running command: blastn -query OceanDNA-b30624/markers.fasta -db /var/lib/cwl/stgc4017d00-0c69-4902-9866-5eb3ad8364b8/dqc_reference/reference_markers.fasta -out OceanDNA-b30624/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:56,491] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:56,491] [INFO] Selected 26 target genomes.
[2023-03-16 03:47:56,492] [INFO] Target genome list was writen to OceanDNA-b30624/target_genomes.txt
[2023-03-16 03:47:56,507] [INFO] Task started: fastANI
[2023-03-16 03:47:56,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c90d075-4898-4402-a549-5f70cf70ffb3/OceanDNA-b30624.fa --refList OceanDNA-b30624/target_genomes.txt --output OceanDNA-b30624/fastani_result.tsv --threads 1
[2023-03-16 03:48:13,519] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:13,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4017d00-0c69-4902-9866-5eb3ad8364b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:13,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4017d00-0c69-4902-9866-5eb3ad8364b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:13,529] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:13,529] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:13,529] [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
Amylibacter kogurei	strain=4G11	GCA_002742285.1	1889778	1889778	type	True	76.3546	107	1013	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.2661	71	1013	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.2358	84	1013	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.2282	83	1013	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	76.2055	92	1013	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	76.0859	59	1013	95	below_threshold
Nereida ignava	strain=CECT 5292	GCA_001049735.1	282199	282199	type	True	76.0776	51	1013	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	76.0283	77	1013	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	76.0253	78	1013	95	below_threshold
Falsihalocynthiibacter arcticus	strain=PAMC 20958	GCA_000812665.2	1579316	1579316	type	True	76.0096	58	1013	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	75.9269	71	1013	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	75.8714	60	1013	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	75.8084	64	1013	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	75.6856	56	1013	95	below_threshold
Aquimixticola soesokkakensis	strain=CECT 8620	GCA_900172375.1	1519096	1519096	type	True	75.3664	52	1013	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:13,529] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30624/tc_result.tsv
[2023-03-16 03:48:13,529] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:13,529] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:13,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4017d00-0c69-4902-9866-5eb3ad8364b8/dqc_reference/checkm_data
[2023-03-16 03:48:13,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:13,534] [INFO] Task started: CheckM
[2023-03-16 03:48:13,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30624/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30624/checkm_input OceanDNA-b30624/checkm_result
[2023-03-16 03:49:04,108] [INFO] Task succeeded: CheckM
[2023-03-16 03:49:04,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:49:04,111] [INFO] ===== Completeness check finished =====
[2023-03-16 03:49:04,111] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:49:04,112] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30624/markers.fasta)
[2023-03-16 03:49:04,112] [INFO] Task started: Blastn
[2023-03-16 03:49:04,112] [INFO] Running command: blastn -query OceanDNA-b30624/markers.fasta -db /var/lib/cwl/stgc4017d00-0c69-4902-9866-5eb3ad8364b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30624/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:49:05,569] [INFO] Task succeeded: Blastn
[2023-03-16 03:49:05,570] [INFO] Selected 20 target genomes.
[2023-03-16 03:49:05,570] [INFO] Target genome list was writen to OceanDNA-b30624/target_genomes_gtdb.txt
[2023-03-16 03:49:05,649] [INFO] Task started: fastANI
[2023-03-16 03:49:05,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c90d075-4898-4402-a549-5f70cf70ffb3/OceanDNA-b30624.fa --refList OceanDNA-b30624/target_genomes_gtdb.txt --output OceanDNA-b30624/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:49:17,452] [INFO] Task succeeded: fastANI
[2023-03-16 03:49:17,461] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:49:17,461] [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
GCA_018607905.1	s__Amylibacter sp002387535	99.863	914	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.84	99.84	0.91	0.91	2	conclusive
GCF_014643735.1	s__Amylibacter cionae	77.5705	258	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719615.1	s__Amylibacter sediminis	77.2696	248	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223125.1	s__Amylibacter sp018223125	77.2234	223	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860325.1	s__Amylibacter lutimaris	77.1171	242	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003447515.1	s__Amylibacter sp003447515	77.0136	135	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002732995.1	s__Profundibacter sp002732995	76.3326	68	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622325.1	s__Sulfitobacter geojensis	76.2282	83	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_900129235.1	s__Litoreibacter ascidiaceicola	76.0963	69	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	76.0662	69	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	76.0253	78	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000812665.2	s__Halocynthiibacter_B arcticus	76.0186	59	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313015.1	s__OMPR01 sp900313015	75.917	58	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__OMPR01	95.0	97.69	97.65	0.92	0.91	5	-
GCF_900172375.1	s__Aquimixticola soesokkakensis	75.3886	53	1013	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquimixticola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:49:17,461] [INFO] GTDB search result was written to OceanDNA-b30624/result_gtdb.tsv
[2023-03-16 03:49:17,461] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:49:17,463] [INFO] DFAST_QC result json was written to OceanDNA-b30624/dqc_result.json
[2023-03-16 03:49:17,463] [INFO] DFAST_QC completed!
[2023-03-16 03:49:17,463] [INFO] Total running time: 0h1m43s