[2023-03-15 04:45:50,549] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:50,551] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:50,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b197135-ab9a-4d19-ae00-4348f49a6a19/dqc_reference
[2023-03-15 04:45:51,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:51,677] [INFO] Task started: Prodigal
[2023-03-15 04:45:51,678] [INFO] Running command: cat /var/lib/cwl/stg390100f8-b1eb-4cc4-82e5-de0e17fb4ea6/OceanDNA-b23634.fa | prodigal -d OceanDNA-b23634/cds.fna -a OceanDNA-b23634/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:46:13,115] [INFO] Task succeeded: Prodigal
[2023-03-15 04:46:13,115] [INFO] Task started: HMMsearch
[2023-03-15 04:46:13,115] [INFO] Running command: hmmsearch --tblout OceanDNA-b23634/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b197135-ab9a-4d19-ae00-4348f49a6a19/dqc_reference/reference_markers.hmm OceanDNA-b23634/protein.faa > /dev/null
[2023-03-15 04:46:13,322] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:46:13,322] [INFO] Found 6/6 markers.
[2023-03-15 04:46:13,366] [INFO] Query marker FASTA was written to OceanDNA-b23634/markers.fasta
[2023-03-15 04:46:13,367] [INFO] Task started: Blastn
[2023-03-15 04:46:13,367] [INFO] Running command: blastn -query OceanDNA-b23634/markers.fasta -db /var/lib/cwl/stg7b197135-ab9a-4d19-ae00-4348f49a6a19/dqc_reference/reference_markers.fasta -out OceanDNA-b23634/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:14,224] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:14,229] [INFO] Selected 16 target genomes.
[2023-03-15 04:46:14,229] [INFO] Target genome list was writen to OceanDNA-b23634/target_genomes.txt
[2023-03-15 04:46:14,239] [INFO] Task started: fastANI
[2023-03-15 04:46:14,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg390100f8-b1eb-4cc4-82e5-de0e17fb4ea6/OceanDNA-b23634.fa --refList OceanDNA-b23634/target_genomes.txt --output OceanDNA-b23634/fastani_result.tsv --threads 1
[2023-03-15 04:46:26,700] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:26,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b197135-ab9a-4d19-ae00-4348f49a6a19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:46:26,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b197135-ab9a-4d19-ae00-4348f49a6a19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:46:26,710] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:46:26,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:46:26,710] [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
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	84.4233	887	1130	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	82.4411	778	1130	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	78.3621	433	1130	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.3307	408	1130	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	78.3016	379	1130	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.0765	398	1130	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	77.9772	404	1130	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	77.5467	261	1130	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	77.5335	281	1130	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	77.5256	259	1130	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	76.5299	176	1130	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.0189	74	1130	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	75.9952	131	1130	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.8349	119	1130	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	75.7822	76	1130	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.5517	69	1130	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:46:26,712] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23634/tc_result.tsv
[2023-03-15 04:46:26,713] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:46:26,713] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:46:26,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b197135-ab9a-4d19-ae00-4348f49a6a19/dqc_reference/checkm_data
[2023-03-15 04:46:26,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:46:26,722] [INFO] Task started: CheckM
[2023-03-15 04:46:26,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23634/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23634/checkm_input OceanDNA-b23634/checkm_result
[2023-03-15 04:47:19,562] [INFO] Task succeeded: CheckM
[2023-03-15 04:47:19,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:47:19,587] [INFO] ===== Completeness check finished =====
[2023-03-15 04:47:19,587] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:47:19,587] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23634/markers.fasta)
[2023-03-15 04:47:19,588] [INFO] Task started: Blastn
[2023-03-15 04:47:19,589] [INFO] Running command: blastn -query OceanDNA-b23634/markers.fasta -db /var/lib/cwl/stg7b197135-ab9a-4d19-ae00-4348f49a6a19/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23634/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:47:21,260] [INFO] Task succeeded: Blastn
[2023-03-15 04:47:21,266] [INFO] Selected 6 target genomes.
[2023-03-15 04:47:21,266] [INFO] Target genome list was writen to OceanDNA-b23634/target_genomes_gtdb.txt
[2023-03-15 04:47:21,271] [INFO] Task started: fastANI
[2023-03-15 04:47:21,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg390100f8-b1eb-4cc4-82e5-de0e17fb4ea6/OceanDNA-b23634.fa --refList OceanDNA-b23634/target_genomes_gtdb.txt --output OceanDNA-b23634/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:47:26,509] [INFO] Task succeeded: fastANI
[2023-03-15 04:47:26,514] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:47:26,514] [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_018402285.1	s__Hyphomonas sp018402285	89.9603	851	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823385.1	s__Hyphomonas sp013823385	85.5343	882	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013025.1	s__Hyphomonas neptunium	85.4758	911	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002841155.1	s__Hyphomonas sp002841155	85.1985	882	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685315.1	s__Hyphomonas polymorpha	84.4233	887	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.45	98.45	0.90	0.90	2	-
GCA_002282565.1	s__Hyphomonas sp002282565	84.3346	632	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:47:26,517] [INFO] GTDB search result was written to OceanDNA-b23634/result_gtdb.tsv
[2023-03-15 04:47:26,522] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:47:26,526] [INFO] DFAST_QC result json was written to OceanDNA-b23634/dqc_result.json
[2023-03-15 04:47:26,526] [INFO] DFAST_QC completed!
[2023-03-15 04:47:26,526] [INFO] Total running time: 0h1m36s