[2023-03-18 02:27:59,069] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:59,069] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:59,069] [INFO] DQC Reference Directory: /var/lib/cwl/stge4b94d6d-33c9-4b74-985b-15e5cde70e60/dqc_reference
[2023-03-18 02:28:00,170] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:28:00,170] [INFO] Task started: Prodigal
[2023-03-18 02:28:00,171] [INFO] Running command: cat /var/lib/cwl/stg9fd3b86f-6ea2-41d1-b6db-fdcbf6e20f19/OceanDNA-b17133.fa | prodigal -d OceanDNA-b17133/cds.fna -a OceanDNA-b17133/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:13,805] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:13,805] [INFO] Task started: HMMsearch
[2023-03-18 02:28:13,805] [INFO] Running command: hmmsearch --tblout OceanDNA-b17133/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4b94d6d-33c9-4b74-985b-15e5cde70e60/dqc_reference/reference_markers.hmm OceanDNA-b17133/protein.faa > /dev/null
[2023-03-18 02:28:13,990] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:13,990] [INFO] Found 6/6 markers.
[2023-03-18 02:28:14,004] [INFO] Query marker FASTA was written to OceanDNA-b17133/markers.fasta
[2023-03-18 02:28:14,004] [INFO] Task started: Blastn
[2023-03-18 02:28:14,004] [INFO] Running command: blastn -query OceanDNA-b17133/markers.fasta -db /var/lib/cwl/stge4b94d6d-33c9-4b74-985b-15e5cde70e60/dqc_reference/reference_markers.fasta -out OceanDNA-b17133/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:14,559] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:14,560] [INFO] Selected 23 target genomes.
[2023-03-18 02:28:14,560] [INFO] Target genome list was writen to OceanDNA-b17133/target_genomes.txt
[2023-03-18 02:28:14,573] [INFO] Task started: fastANI
[2023-03-18 02:28:14,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd3b86f-6ea2-41d1-b6db-fdcbf6e20f19/OceanDNA-b17133.fa --refList OceanDNA-b17133/target_genomes.txt --output OceanDNA-b17133/fastani_result.tsv --threads 1
[2023-03-18 02:28:27,785] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:27,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4b94d6d-33c9-4b74-985b-15e5cde70e60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:27,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4b94d6d-33c9-4b74-985b-15e5cde70e60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:27,791] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:27,791] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:28:27,791] [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
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	76.6443	99	750	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_016918515.1	1506996	1506996	type	True	76.4633	78	750	95	below_threshold
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	76.4488	61	750	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_014201505.1	1506996	1506996	type	True	76.4371	77	750	95	below_threshold
Desulfurivibrio alkaliphilus	strain=AHT 2	GCA_000092205.1	427923	427923	type	True	76.4207	55	750	95	below_threshold
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	76.0844	63	750	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:27,791] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17133/tc_result.tsv
[2023-03-18 02:28:27,791] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:27,792] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:27,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4b94d6d-33c9-4b74-985b-15e5cde70e60/dqc_reference/checkm_data
[2023-03-18 02:28:27,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:27,795] [INFO] Task started: CheckM
[2023-03-18 02:28:27,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17133/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17133/checkm_input OceanDNA-b17133/checkm_result
[2023-03-18 02:29:05,393] [INFO] Task succeeded: CheckM
[2023-03-18 02:29:05,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:29:05,395] [INFO] ===== Completeness check finished =====
[2023-03-18 02:29:05,395] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:29:05,395] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17133/markers.fasta)
[2023-03-18 02:29:05,395] [INFO] Task started: Blastn
[2023-03-18 02:29:05,395] [INFO] Running command: blastn -query OceanDNA-b17133/markers.fasta -db /var/lib/cwl/stge4b94d6d-33c9-4b74-985b-15e5cde70e60/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17133/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:29:06,256] [INFO] Task succeeded: Blastn
[2023-03-18 02:29:06,257] [INFO] Selected 28 target genomes.
[2023-03-18 02:29:06,257] [INFO] Target genome list was writen to OceanDNA-b17133/target_genomes_gtdb.txt
[2023-03-18 02:29:06,284] [INFO] Task started: fastANI
[2023-03-18 02:29:06,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd3b86f-6ea2-41d1-b6db-fdcbf6e20f19/OceanDNA-b17133.fa --refList OceanDNA-b17133/target_genomes_gtdb.txt --output OceanDNA-b17133/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:29:20,470] [INFO] Task succeeded: fastANI
[2023-03-18 02:29:20,481] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:29:20,481] [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_014381505.1	s__Desulfatifera sulfidica	79.2649	303	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfatifera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887485.1	s__UBA2270 sp903887485	76.983	132	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	99.90	99.87	0.96	0.96	3	-
GCA_018821985.1	s__UBA2270 sp018821985	76.9401	113	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	99.96	99.93	0.98	0.98	3	-
GCA_003604995.1	s__UBA10518 sp003604995	76.9305	55	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903891045.1	s__UBA2270 sp903891045	76.9039	110	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	99.69	99.69	0.87	0.87	2	-
GCA_002347085.1	s__UBA2270 sp002347085	76.8889	81	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327225.1	s__UBA2270 sp002327225	76.6471	92	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429965.1	s__Desulfobulbus_A mediterraneus	76.6443	99	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000769715.1	s__Desulfoprunum sp000769715	76.6071	85	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	99.79	99.74	0.93	0.93	5	-
GCA_015484845.1	s__DRKI01 sp015484845	76.5974	117	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051875.1	s__DRKI01 sp011051875	76.522	94	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	99.14	99.09	0.93	0.90	3	-
GCA_013426795.1	s__UBA2270 sp013426795	76.4308	124	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201505.1	s__Desulfoprunum benzoelyticum	76.4105	78	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_015486315.1	s__Desulfobulbus_C sp015486315	76.3989	50	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933635.1	s__Desulfoprunum sp008933635	76.3615	73	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816555.1	s__SURF-16 sp018816555	76.1297	59	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773475.1	s__UBA2270 sp009773475	76.0787	106	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841785.1	s__UBA2262 sp002841785	76.025	50	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	98.87	98.69	0.72	0.70	5	-
GCA_018897105.1	s__SURF-16 sp018897105	75.9917	58	750	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	99.97	99.97	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-18 02:29:20,482] [INFO] GTDB search result was written to OceanDNA-b17133/result_gtdb.tsv
[2023-03-18 02:29:20,482] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:29:20,483] [INFO] DFAST_QC result json was written to OceanDNA-b17133/dqc_result.json
[2023-03-18 02:29:20,483] [INFO] DFAST_QC completed!
[2023-03-18 02:29:20,483] [INFO] Total running time: 0h1m21s