[2023-03-15 17:46:31,717] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,717] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg5acd5c9e-df3b-4143-90a4-6834087aab9f/dqc_reference
[2023-03-15 17:46:32,840] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,840] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,840] [INFO] Running command: cat /var/lib/cwl/stga840307e-1b74-465e-989e-a7bcc823b954/OceanDNA-b22811.fa | prodigal -d OceanDNA-b22811/cds.fna -a OceanDNA-b22811/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:49,695] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:49,696] [INFO] Task started: HMMsearch
[2023-03-15 17:46:49,696] [INFO] Running command: hmmsearch --tblout OceanDNA-b22811/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5acd5c9e-df3b-4143-90a4-6834087aab9f/dqc_reference/reference_markers.hmm OceanDNA-b22811/protein.faa > /dev/null
[2023-03-15 17:46:49,897] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:49,897] [INFO] Found 6/6 markers.
[2023-03-15 17:46:49,924] [INFO] Query marker FASTA was written to OceanDNA-b22811/markers.fasta
[2023-03-15 17:46:49,925] [INFO] Task started: Blastn
[2023-03-15 17:46:49,925] [INFO] Running command: blastn -query OceanDNA-b22811/markers.fasta -db /var/lib/cwl/stg5acd5c9e-df3b-4143-90a4-6834087aab9f/dqc_reference/reference_markers.fasta -out OceanDNA-b22811/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:50,516] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:50,519] [INFO] Selected 32 target genomes.
[2023-03-15 17:46:50,519] [INFO] Target genome list was writen to OceanDNA-b22811/target_genomes.txt
[2023-03-15 17:46:50,540] [INFO] Task started: fastANI
[2023-03-15 17:46:50,540] [INFO] Running command: fastANI --query /var/lib/cwl/stga840307e-1b74-465e-989e-a7bcc823b954/OceanDNA-b22811.fa --refList OceanDNA-b22811/target_genomes.txt --output OceanDNA-b22811/fastani_result.tsv --threads 1
[2023-03-15 17:47:15,984] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:15,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5acd5c9e-df3b-4143-90a4-6834087aab9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:47:15,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5acd5c9e-df3b-4143-90a4-6834087aab9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:47:15,995] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:47:15,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:47:15,996] [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	75.8589	164	940	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.6806	128	940	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.6609	94	940	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.4647	115	940	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.4302	79	940	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.2975	113	940	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	75.2956	111	940	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.2942	73	940	95	below_threshold
Limnoglobus roseus	strain=PX52	GCA_008254045.1	2598579	2598579	type	True	74.9224	107	940	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	74.8688	54	940	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	74.6938	68	940	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	74.6859	79	940	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	74.6857	81	940	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	74.6626	121	940	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	74.6352	52	940	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	74.6296	68	940	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	74.6233	81	940	95	below_threshold
Streptomyces laurentii	strain=ATCC 31255	GCA_002355495.1	39478	39478	type	True	74.6115	100	940	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	74.5957	52	940	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:47:15,996] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22811/tc_result.tsv
[2023-03-15 17:47:15,997] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:47:15,997] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:47:15,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5acd5c9e-df3b-4143-90a4-6834087aab9f/dqc_reference/checkm_data
[2023-03-15 17:47:15,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:47:16,077] [INFO] Task started: CheckM
[2023-03-15 17:47:16,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22811/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22811/checkm_input OceanDNA-b22811/checkm_result
[2023-03-15 17:47:59,441] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:59,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:59,444] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:59,444] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:59,444] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22811/markers.fasta)
[2023-03-15 17:47:59,445] [INFO] Task started: Blastn
[2023-03-15 17:47:59,445] [INFO] Running command: blastn -query OceanDNA-b22811/markers.fasta -db /var/lib/cwl/stg5acd5c9e-df3b-4143-90a4-6834087aab9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22811/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:48:00,292] [INFO] Task succeeded: Blastn
[2023-03-15 17:48:00,293] [INFO] Selected 30 target genomes.
[2023-03-15 17:48:00,293] [INFO] Target genome list was writen to OceanDNA-b22811/target_genomes_gtdb.txt
[2023-03-15 17:48:00,414] [INFO] Task started: fastANI
[2023-03-15 17:48:00,414] [INFO] Running command: fastANI --query /var/lib/cwl/stga840307e-1b74-465e-989e-a7bcc823b954/OceanDNA-b22811.fa --refList OceanDNA-b22811/target_genomes_gtdb.txt --output OceanDNA-b22811/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:48:24,629] [INFO] Task succeeded: fastANI
[2023-03-15 17:48:24,636] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:48:24,636] [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	75.8266	168	940	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	75.6631	130	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610835.1	s__Planctomyces_A sp001610835	75.4568	124	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798445.1	s__SXKJ01 sp005798445	75.4048	50	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.80	99.80	0.90	0.90	2	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.3375	71	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.306	86	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.0852	81	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	75.0646	94	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970785.1	s__F1-20-MAGs016 sp018970785	75.0421	67	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200145.1	s__JACQFH01 sp016200145	74.9527	57	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACQFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	74.9519	162	940	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213895.1	s__JACQZJ01 sp016213895	74.718	60	940	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JACQZJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:48:24,636] [INFO] GTDB search result was written to OceanDNA-b22811/result_gtdb.tsv
[2023-03-15 17:48:24,636] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:48:24,638] [INFO] DFAST_QC result json was written to OceanDNA-b22811/dqc_result.json
[2023-03-15 17:48:24,638] [INFO] DFAST_QC completed!
[2023-03-15 17:48:24,638] [INFO] Total running time: 0h1m53s