[2023-03-16 06:03:00,928] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:03:00,931] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:03:00,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg4355d92d-5258-47de-bffb-8d9225504b4a/dqc_reference
[2023-03-16 06:03:02,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:03:02,061] [INFO] Task started: Prodigal
[2023-03-16 06:03:02,062] [INFO] Running command: cat /var/lib/cwl/stg989b2e15-e5d6-43b2-b013-6bcd41e5edcd/OceanDNA-b23484.fa | prodigal -d OceanDNA-b23484/cds.fna -a OceanDNA-b23484/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:03:24,415] [INFO] Task succeeded: Prodigal
[2023-03-16 06:03:24,416] [INFO] Task started: HMMsearch
[2023-03-16 06:03:24,416] [INFO] Running command: hmmsearch --tblout OceanDNA-b23484/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4355d92d-5258-47de-bffb-8d9225504b4a/dqc_reference/reference_markers.hmm OceanDNA-b23484/protein.faa > /dev/null
[2023-03-16 06:03:24,641] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:03:24,641] [INFO] Found 6/6 markers.
[2023-03-16 06:03:24,672] [INFO] Query marker FASTA was written to OceanDNA-b23484/markers.fasta
[2023-03-16 06:03:24,673] [INFO] Task started: Blastn
[2023-03-16 06:03:24,674] [INFO] Running command: blastn -query OceanDNA-b23484/markers.fasta -db /var/lib/cwl/stg4355d92d-5258-47de-bffb-8d9225504b4a/dqc_reference/reference_markers.fasta -out OceanDNA-b23484/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:25,325] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:25,331] [INFO] Selected 25 target genomes.
[2023-03-16 06:03:25,331] [INFO] Target genome list was writen to OceanDNA-b23484/target_genomes.txt
[2023-03-16 06:03:25,348] [INFO] Task started: fastANI
[2023-03-16 06:03:25,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg989b2e15-e5d6-43b2-b013-6bcd41e5edcd/OceanDNA-b23484.fa --refList OceanDNA-b23484/target_genomes.txt --output OceanDNA-b23484/fastani_result.tsv --threads 1
[2023-03-16 06:03:40,384] [INFO] Task succeeded: fastANI
[2023-03-16 06:03:40,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4355d92d-5258-47de-bffb-8d9225504b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:03:40,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4355d92d-5258-47de-bffb-8d9225504b4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:03:40,393] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:03:40,393] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:03:40,394] [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
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	79.5564	79	1208	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	76.4038	58	1208	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	76.3658	60	1208	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	76.3126	53	1208	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	76.2827	78	1208	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	76.2598	67	1208	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	76.2197	61	1208	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	76.1521	64	1208	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	76.0042	77	1208	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	75.9219	73	1208	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	75.8699	74	1208	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	75.7391	74	1208	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:03:40,395] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23484/tc_result.tsv
[2023-03-16 06:03:40,395] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:03:40,395] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:03:40,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4355d92d-5258-47de-bffb-8d9225504b4a/dqc_reference/checkm_data
[2023-03-16 06:03:40,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:03:40,553] [INFO] Task started: CheckM
[2023-03-16 06:03:40,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23484/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23484/checkm_input OceanDNA-b23484/checkm_result
[2023-03-16 06:04:36,494] [INFO] Task succeeded: CheckM
[2023-03-16 06:04:36,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:04:36,517] [INFO] ===== Completeness check finished =====
[2023-03-16 06:04:36,518] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:04:36,518] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23484/markers.fasta)
[2023-03-16 06:04:36,519] [INFO] Task started: Blastn
[2023-03-16 06:04:36,519] [INFO] Running command: blastn -query OceanDNA-b23484/markers.fasta -db /var/lib/cwl/stg4355d92d-5258-47de-bffb-8d9225504b4a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23484/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:04:37,659] [INFO] Task succeeded: Blastn
[2023-03-16 06:04:37,669] [INFO] Selected 26 target genomes.
[2023-03-16 06:04:37,669] [INFO] Target genome list was writen to OceanDNA-b23484/target_genomes_gtdb.txt
[2023-03-16 06:04:37,783] [INFO] Task started: fastANI
[2023-03-16 06:04:37,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg989b2e15-e5d6-43b2-b013-6bcd41e5edcd/OceanDNA-b23484.fa --refList OceanDNA-b23484/target_genomes_gtdb.txt --output OceanDNA-b23484/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:04:51,984] [INFO] Task succeeded: fastANI
[2023-03-16 06:04:51,993] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:04:51,994] [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_017642885.1	s__Henriciella sp017642885	80.1321	65	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.99	99.99	0.96	0.96	2	-
GCF_001854405.1	s__Henriciella sp001854405	77.0536	80	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222605.1	s__Hyphomonas sp002695785	76.767	63	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCA_002733705.1	s__Henriciella sp002733705	76.4814	70	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_000685235.1	s__Hyphomonas adhaerens	76.4038	58	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
GCF_000685275.1	s__Hyphomonas johnsonii	76.3487	52	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576285.1	s__Henriciella sp003576285	76.1543	69	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCF_000682755.1	s__Hyphomonas beringensis	76.1521	64	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214545.1	s__Henriciella sp013214545	76.1334	64	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	76.0248	76	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018827375.1	s__Hyphomonas sp018827375	75.9714	63	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.92	99.88	0.98	0.97	4	-
GCA_002414505.1	s__Hyphomonas sp002414505	75.9189	61	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	-
GCA_002408125.1	s__UBA5336 sp002408125	75.9076	65	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA5336	95.0	99.93	99.87	0.96	0.95	4	-
GCF_002088945.1	s__Henriciella pelagia	75.8681	74	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016125515.1	s__Hyphomonas sp016125515	75.8223	56	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088975.1	s__Henriciella aquimarina	75.7391	74	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:04:51,996] [INFO] GTDB search result was written to OceanDNA-b23484/result_gtdb.tsv
[2023-03-16 06:04:52,003] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:04:52,007] [INFO] DFAST_QC result json was written to OceanDNA-b23484/dqc_result.json
[2023-03-16 06:04:52,007] [INFO] DFAST_QC completed!
[2023-03-16 06:04:52,007] [INFO] Total running time: 0h1m51s