[2023-03-18 08:55:50,552] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,552] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg50917c53-4bf8-490f-b376-e2c8c9a865bd/dqc_reference
[2023-03-18 08:55:51,799] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,800] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,800] [INFO] Running command: cat /var/lib/cwl/stg1ee7cccf-11b0-4365-a9b6-bf14ce441187/OceanDNA-b1714.fa | prodigal -d OceanDNA-b1714/cds.fna -a OceanDNA-b1714/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:11,801] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:11,802] [INFO] Task started: HMMsearch
[2023-03-18 08:56:11,802] [INFO] Running command: hmmsearch --tblout OceanDNA-b1714/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50917c53-4bf8-490f-b376-e2c8c9a865bd/dqc_reference/reference_markers.hmm OceanDNA-b1714/protein.faa > /dev/null
[2023-03-18 08:56:12,027] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:12,028] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1ee7cccf-11b0-4365-a9b6-bf14ce441187/OceanDNA-b1714.fa]
[2023-03-18 08:56:12,055] [INFO] Query marker FASTA was written to OceanDNA-b1714/markers.fasta
[2023-03-18 08:56:12,055] [INFO] Task started: Blastn
[2023-03-18 08:56:12,056] [INFO] Running command: blastn -query OceanDNA-b1714/markers.fasta -db /var/lib/cwl/stg50917c53-4bf8-490f-b376-e2c8c9a865bd/dqc_reference/reference_markers.fasta -out OceanDNA-b1714/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:12,558] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:12,559] [INFO] Selected 15 target genomes.
[2023-03-18 08:56:12,559] [INFO] Target genome list was writen to OceanDNA-b1714/target_genomes.txt
[2023-03-18 08:56:12,570] [INFO] Task started: fastANI
[2023-03-18 08:56:12,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ee7cccf-11b0-4365-a9b6-bf14ce441187/OceanDNA-b1714.fa --refList OceanDNA-b1714/target_genomes.txt --output OceanDNA-b1714/fastani_result.tsv --threads 1
[2023-03-18 08:56:23,613] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:23,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50917c53-4bf8-490f-b376-e2c8c9a865bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:23,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50917c53-4bf8-490f-b376-e2c8c9a865bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:23,620] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:23,620] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:56:23,620] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.5679	93	944	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	74.8526	61	944	95	below_threshold
Geodermatophilus amargosae	strain=DSM 46136	GCA_900116515.1	1296565	1296565	type	True	74.8211	80	944	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	74.8093	55	944	95	below_threshold
Pseudonocardia endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	74.6996	72	944	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	74.653	54	944	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	74.6319	54	944	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	74.6282	56	944	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	74.6114	63	944	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:56:23,621] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1714/tc_result.tsv
[2023-03-18 08:56:23,621] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:23,621] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:23,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50917c53-4bf8-490f-b376-e2c8c9a865bd/dqc_reference/checkm_data
[2023-03-18 08:56:23,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:23,649] [INFO] Task started: CheckM
[2023-03-18 08:56:23,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1714/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1714/checkm_input OceanDNA-b1714/checkm_result
[2023-03-18 08:57:12,165] [INFO] Task succeeded: CheckM
[2023-03-18 08:57:12,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:57:12,168] [INFO] ===== Completeness check finished =====
[2023-03-18 08:57:12,168] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:57:12,168] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1714/markers.fasta)
[2023-03-18 08:57:12,170] [INFO] Task started: Blastn
[2023-03-18 08:57:12,170] [INFO] Running command: blastn -query OceanDNA-b1714/markers.fasta -db /var/lib/cwl/stg50917c53-4bf8-490f-b376-e2c8c9a865bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1714/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:57:12,873] [INFO] Task succeeded: Blastn
[2023-03-18 08:57:12,873] [INFO] Selected 16 target genomes.
[2023-03-18 08:57:12,874] [INFO] Target genome list was writen to OceanDNA-b1714/target_genomes_gtdb.txt
[2023-03-18 08:57:12,884] [INFO] Task started: fastANI
[2023-03-18 08:57:12,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ee7cccf-11b0-4365-a9b6-bf14ce441187/OceanDNA-b1714.fa --refList OceanDNA-b1714/target_genomes_gtdb.txt --output OceanDNA-b1714/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:57:21,696] [INFO] Task succeeded: fastANI
[2023-03-18 08:57:21,701] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:57:21,702] [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_905182135.1	s__UBA10347 sp905182135	76.2031	56	944	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA10347;g__UBA10347	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003485885.1	s__UBA10347 sp003485885	76.1877	93	944	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA10347;g__UBA10347	95.0	98.91	98.91	0.90	0.90	2	-
GCA_013002375.1	s__JABDJW01 sp013002375	75.7543	75	944	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SHLQ01;g__JABDJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649895.1	s__Actinomarinicola sp016649895	75.7426	71	944	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903953195.1	s__SXMI01 sp903953195	75.4859	52	944	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	98.58	98.55	0.81	0.80	3	-
GCA_016703525.1	s__JADJBW01 sp016703525	75.3422	60	944	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__JADJBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805555.1	s__CADCSY01 sp902805555	75.026	53	944	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746395.1	s__Streptomyces mirabilis_A	74.7614	79	944	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:57:21,702] [INFO] GTDB search result was written to OceanDNA-b1714/result_gtdb.tsv
[2023-03-18 08:57:21,702] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:57:21,703] [INFO] DFAST_QC result json was written to OceanDNA-b1714/dqc_result.json
[2023-03-18 08:57:21,703] [INFO] DFAST_QC completed!
[2023-03-18 08:57:21,703] [INFO] Total running time: 0h1m31s