[2023-03-18 08:36:16,003] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,003] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg83aded09-17be-4488-be86-a07fc07b4257/dqc_reference
[2023-03-18 08:36:17,827] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,827] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,827] [INFO] Running command: cat /var/lib/cwl/stg8627c9a4-0716-44f8-ba65-1148740c8b83/OceanDNA-b22812.fa | prodigal -d OceanDNA-b22812/cds.fna -a OceanDNA-b22812/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:30,913] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:30,914] [INFO] Task started: HMMsearch
[2023-03-18 08:36:30,914] [INFO] Running command: hmmsearch --tblout OceanDNA-b22812/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83aded09-17be-4488-be86-a07fc07b4257/dqc_reference/reference_markers.hmm OceanDNA-b22812/protein.faa > /dev/null
[2023-03-18 08:36:31,127] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:31,128] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8627c9a4-0716-44f8-ba65-1148740c8b83/OceanDNA-b22812.fa]
[2023-03-18 08:36:31,152] [INFO] Query marker FASTA was written to OceanDNA-b22812/markers.fasta
[2023-03-18 08:36:31,153] [INFO] Task started: Blastn
[2023-03-18 08:36:31,153] [INFO] Running command: blastn -query OceanDNA-b22812/markers.fasta -db /var/lib/cwl/stg83aded09-17be-4488-be86-a07fc07b4257/dqc_reference/reference_markers.fasta -out OceanDNA-b22812/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:31,767] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:31,768] [INFO] Selected 21 target genomes.
[2023-03-18 08:36:31,768] [INFO] Target genome list was writen to OceanDNA-b22812/target_genomes.txt
[2023-03-18 08:36:31,833] [INFO] Task started: fastANI
[2023-03-18 08:36:31,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg8627c9a4-0716-44f8-ba65-1148740c8b83/OceanDNA-b22812.fa --refList OceanDNA-b22812/target_genomes.txt --output OceanDNA-b22812/fastani_result.tsv --threads 1
[2023-03-18 08:36:50,108] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:50,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83aded09-17be-4488-be86-a07fc07b4257/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:50,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83aded09-17be-4488-be86-a07fc07b4257/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:50,115] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:50,116] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:36:50,116] [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
Alienimonas californiensis	strain=CA12	GCA_007743815.1	2527989	2527989	type	True	75.4602	81	659	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.4451	62	659	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	75.3088	53	659	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.095	55	659	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8911	72	659	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8517	75	659	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.7416	68	659	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	74.7366	53	659	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.6125	60	659	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:36:50,139] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22812/tc_result.tsv
[2023-03-18 08:36:50,179] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:50,179] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:50,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83aded09-17be-4488-be86-a07fc07b4257/dqc_reference/checkm_data
[2023-03-18 08:36:50,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:50,185] [INFO] Task started: CheckM
[2023-03-18 08:36:50,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22812/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22812/checkm_input OceanDNA-b22812/checkm_result
[2023-03-18 08:37:26,118] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:26,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.56%
Contamintation: 7.29%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 08:37:26,125] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:26,125] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:26,125] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22812/markers.fasta)
[2023-03-18 08:37:26,126] [INFO] Task started: Blastn
[2023-03-18 08:37:26,126] [INFO] Running command: blastn -query OceanDNA-b22812/markers.fasta -db /var/lib/cwl/stg83aded09-17be-4488-be86-a07fc07b4257/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22812/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:27,167] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:27,169] [INFO] Selected 24 target genomes.
[2023-03-18 08:37:27,169] [INFO] Target genome list was writen to OceanDNA-b22812/target_genomes_gtdb.txt
[2023-03-18 08:37:27,189] [INFO] Task started: fastANI
[2023-03-18 08:37:27,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg8627c9a4-0716-44f8-ba65-1148740c8b83/OceanDNA-b22812.fa --refList OceanDNA-b22812/target_genomes_gtdb.txt --output OceanDNA-b22812/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:50,076] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:50,083] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:37:50,083] [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_007743815.1	s__Alienimonas californiensis	75.4603	81	659	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.4287	63	659	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013036045.1	s__Alienimonas chondri	75.3088	53	659	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610835.1	s__Planctomyces_A sp001610835	75.2064	60	659	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	74.8799	74	659	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752535.1	s__Tautonia plasticadhaerens	74.8445	76	659	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308215.1	s__Urbifossiella sp017308215	74.7832	73	659	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087625.1	s__Aquisphaera giovannonii	74.7416	68	659	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977685.1	s__Tautonia sociabilis	74.7366	53	659	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794545.1	s__JABFXX01 sp016794545	74.614	58	659	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:50,085] [INFO] GTDB search result was written to OceanDNA-b22812/result_gtdb.tsv
[2023-03-18 08:37:50,085] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:50,087] [INFO] DFAST_QC result json was written to OceanDNA-b22812/dqc_result.json
[2023-03-18 08:37:50,087] [INFO] DFAST_QC completed!
[2023-03-18 08:37:50,087] [INFO] Total running time: 0h1m34s