[2023-03-15 06:35:36,163] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:35:36,167] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:35:36,167] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f9de0ac-354b-426a-b5e8-42213291f1e2/dqc_reference
[2023-03-15 06:35:37,289] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:35:37,290] [INFO] Task started: Prodigal
[2023-03-15 06:35:37,290] [INFO] Running command: cat /var/lib/cwl/stg942e5ee9-f714-4379-92e5-fd19ca95ccca/OceanDNA-b22815.fa | prodigal -d OceanDNA-b22815/cds.fna -a OceanDNA-b22815/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:35:57,263] [INFO] Task succeeded: Prodigal
[2023-03-15 06:35:57,263] [INFO] Task started: HMMsearch
[2023-03-15 06:35:57,263] [INFO] Running command: hmmsearch --tblout OceanDNA-b22815/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f9de0ac-354b-426a-b5e8-42213291f1e2/dqc_reference/reference_markers.hmm OceanDNA-b22815/protein.faa > /dev/null
[2023-03-15 06:35:57,472] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:35:57,473] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg942e5ee9-f714-4379-92e5-fd19ca95ccca/OceanDNA-b22815.fa]
[2023-03-15 06:35:57,510] [INFO] Query marker FASTA was written to OceanDNA-b22815/markers.fasta
[2023-03-15 06:35:57,511] [INFO] Task started: Blastn
[2023-03-15 06:35:57,511] [INFO] Running command: blastn -query OceanDNA-b22815/markers.fasta -db /var/lib/cwl/stg2f9de0ac-354b-426a-b5e8-42213291f1e2/dqc_reference/reference_markers.fasta -out OceanDNA-b22815/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:35:58,064] [INFO] Task succeeded: Blastn
[2023-03-15 06:35:58,071] [INFO] Selected 27 target genomes.
[2023-03-15 06:35:58,072] [INFO] Target genome list was writen to OceanDNA-b22815/target_genomes.txt
[2023-03-15 06:35:58,086] [INFO] Task started: fastANI
[2023-03-15 06:35:58,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg942e5ee9-f714-4379-92e5-fd19ca95ccca/OceanDNA-b22815.fa --refList OceanDNA-b22815/target_genomes.txt --output OceanDNA-b22815/fastani_result.tsv --threads 1
[2023-03-15 06:36:21,547] [INFO] Task succeeded: fastANI
[2023-03-15 06:36:21,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f9de0ac-354b-426a-b5e8-42213291f1e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:36:21,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f9de0ac-354b-426a-b5e8-42213291f1e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:36:21,556] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:36:21,556] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:36:21,556] [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
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.4055	70	1041	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.1763	69	1041	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.0937	56	1041	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	74.85	67	1041	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.7853	78	1041	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	74.7673	73	1041	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.7041	95	1041	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.663	72	1041	95	below_threshold
Amycolatopsis dendrobii	strain=DR6-1	GCA_014145675.1	2760662	2760662	type	True	74.6304	73	1041	95	below_threshold
Amycolatopsis rubida	strain=DSM 44637	GCA_900115345.1	112413	112413	type	True	74.5653	82	1041	95	below_threshold
Amycolatopsis nivea	strain=CFH S0261	GCA_004522235.1	1644109	1644109	type	True	74.5142	68	1041	95	below_threshold
Amycolatopsis circi	strain=DSM 45561	GCA_003385235.1	871959	871959	type	True	74.5098	67	1041	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:36:21,559] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22815/tc_result.tsv
[2023-03-15 06:36:21,561] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:36:21,561] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:36:21,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f9de0ac-354b-426a-b5e8-42213291f1e2/dqc_reference/checkm_data
[2023-03-15 06:36:21,562] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:36:21,573] [INFO] Task started: CheckM
[2023-03-15 06:36:21,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22815/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22815/checkm_input OceanDNA-b22815/checkm_result
[2023-03-15 06:37:11,478] [INFO] Task succeeded: CheckM
[2023-03-15 06:37:11,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:37:11,515] [INFO] ===== Completeness check finished =====
[2023-03-15 06:37:11,515] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:37:11,515] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22815/markers.fasta)
[2023-03-15 06:37:11,516] [INFO] Task started: Blastn
[2023-03-15 06:37:11,516] [INFO] Running command: blastn -query OceanDNA-b22815/markers.fasta -db /var/lib/cwl/stg2f9de0ac-354b-426a-b5e8-42213291f1e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22815/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:37:12,287] [INFO] Task succeeded: Blastn
[2023-03-15 06:37:12,295] [INFO] Selected 35 target genomes.
[2023-03-15 06:37:12,295] [INFO] Target genome list was writen to OceanDNA-b22815/target_genomes_gtdb.txt
[2023-03-15 06:37:12,425] [INFO] Task started: fastANI
[2023-03-15 06:37:12,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg942e5ee9-f714-4379-92e5-fd19ca95ccca/OceanDNA-b22815.fa --refList OceanDNA-b22815/target_genomes_gtdb.txt --output OceanDNA-b22815/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:37:37,413] [INFO] Task succeeded: fastANI
[2023-03-15 06:37:37,420] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:37:37,420] [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_007747795.1	s__Maioricimonas rarisocia	75.1763	69	1041	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753265.1	s__Botrimarina mediterranea	75.1061	55	1041	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.0935	60	1041	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	74.8551	66	1041	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752535.1	s__Tautonia plasticadhaerens	74.8005	74	1041	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977685.1	s__Tautonia sociabilis	74.7702	73	1041	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344625.1	s__Solirubrobacter sp003344625	74.7105	62	1041	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182965.1	s__JADJMO01 sp016182965	74.7091	92	1041	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JADJMO01;g__JADJMO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044185.1	s__SEOHO-28 sp003044185	74.6759	69	1041	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	98.17	98.17	0.92	0.92	2	-
GCA_016795345.1	s__JAEUHO01 sp016795345	74.5709	53	1041	d__Bacteria;p__Planctomycetota;c__PLA2;o__PLA2;f__JAEUHO01;g__JAEUHO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:37:37,421] [INFO] GTDB search result was written to OceanDNA-b22815/result_gtdb.tsv
[2023-03-15 06:37:37,421] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:37:37,424] [INFO] DFAST_QC result json was written to OceanDNA-b22815/dqc_result.json
[2023-03-15 06:37:37,424] [INFO] DFAST_QC completed!
[2023-03-15 06:37:37,424] [INFO] Total running time: 0h2m1s