[2023-03-15 11:09:10,789] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,789] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,789] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5cb9863-d2c5-4ebf-8ba6-7bc9473ceb56/dqc_reference
[2023-03-15 11:09:11,986] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:11,986] [INFO] Task started: Prodigal
[2023-03-15 11:09:11,986] [INFO] Running command: cat /var/lib/cwl/stg3e233909-13d0-4a21-910c-1100779310b3/OceanDNA-b21013.fa | prodigal -d OceanDNA-b21013/cds.fna -a OceanDNA-b21013/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:36,313] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:36,314] [INFO] Task started: HMMsearch
[2023-03-15 11:09:36,314] [INFO] Running command: hmmsearch --tblout OceanDNA-b21013/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5cb9863-d2c5-4ebf-8ba6-7bc9473ceb56/dqc_reference/reference_markers.hmm OceanDNA-b21013/protein.faa > /dev/null
[2023-03-15 11:09:36,563] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:36,564] [INFO] Found 6/6 markers.
[2023-03-15 11:09:36,593] [INFO] Query marker FASTA was written to OceanDNA-b21013/markers.fasta
[2023-03-15 11:09:36,601] [INFO] Task started: Blastn
[2023-03-15 11:09:36,601] [INFO] Running command: blastn -query OceanDNA-b21013/markers.fasta -db /var/lib/cwl/stgb5cb9863-d2c5-4ebf-8ba6-7bc9473ceb56/dqc_reference/reference_markers.fasta -out OceanDNA-b21013/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:37,281] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:37,282] [INFO] Selected 26 target genomes.
[2023-03-15 11:09:37,282] [INFO] Target genome list was writen to OceanDNA-b21013/target_genomes.txt
[2023-03-15 11:09:37,298] [INFO] Task started: fastANI
[2023-03-15 11:09:37,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e233909-13d0-4a21-910c-1100779310b3/OceanDNA-b21013.fa --refList OceanDNA-b21013/target_genomes.txt --output OceanDNA-b21013/fastani_result.tsv --threads 1
[2023-03-15 11:10:01,356] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:01,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5cb9863-d2c5-4ebf-8ba6-7bc9473ceb56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:10:01,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5cb9863-d2c5-4ebf-8ba6-7bc9473ceb56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:10:01,371] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:10:01,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:10:01,371] [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
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	75.7194	59	1415	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	75.6532	68	1415	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	75.5134	60	1415	95	below_threshold
Geomonas silvestris	strain=Red330	GCA_014193515.1	2740184	2740184	type	True	75.3595	75	1415	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	75.3521	73	1415	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.2733	136	1415	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	75.2641	167	1415	95	below_threshold
Luteimonas deserti	strain=SJ-16	GCA_013425765.1	2752306	2752306	type	True	75.1774	88	1415	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	75.1093	175	1415	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	75.1069	105	1415	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.0615	131	1415	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	75.0495	110	1415	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	75.042	231	1415	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	75.0366	85	1415	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	75.0332	85	1415	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.0306	127	1415	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	75.0104	179	1415	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.9804	134	1415	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.9461	219	1415	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.9336	286	1415	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	74.9031	216	1415	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.8957	208	1415	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	74.8576	160	1415	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	74.8269	52	1415	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	74.817	106	1415	95	below_threshold
Thermocrispum agreste	strain=DSM 44070	GCA_000427905.1	37925	37925	type	True	74.7275	81	1415	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:10:01,371] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21013/tc_result.tsv
[2023-03-15 11:10:01,371] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:10:01,371] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:10:01,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5cb9863-d2c5-4ebf-8ba6-7bc9473ceb56/dqc_reference/checkm_data
[2023-03-15 11:10:01,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:10:01,378] [INFO] Task started: CheckM
[2023-03-15 11:10:01,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21013/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21013/checkm_input OceanDNA-b21013/checkm_result
[2023-03-15 11:11:11,010] [INFO] Task succeeded: CheckM
[2023-03-15 11:11:11,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:11:11,014] [INFO] ===== Completeness check finished =====
[2023-03-15 11:11:11,014] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:11:11,014] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21013/markers.fasta)
[2023-03-15 11:11:11,014] [INFO] Task started: Blastn
[2023-03-15 11:11:11,014] [INFO] Running command: blastn -query OceanDNA-b21013/markers.fasta -db /var/lib/cwl/stgb5cb9863-d2c5-4ebf-8ba6-7bc9473ceb56/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21013/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:11:12,075] [INFO] Task succeeded: Blastn
[2023-03-15 11:11:12,076] [INFO] Selected 14 target genomes.
[2023-03-15 11:11:12,076] [INFO] Target genome list was writen to OceanDNA-b21013/target_genomes_gtdb.txt
[2023-03-15 11:11:12,089] [INFO] Task started: fastANI
[2023-03-15 11:11:12,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e233909-13d0-4a21-910c-1100779310b3/OceanDNA-b21013.fa --refList OceanDNA-b21013/target_genomes_gtdb.txt --output OceanDNA-b21013/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:11:22,857] [INFO] Task succeeded: fastANI
[2023-03-15 11:11:22,865] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:11:22,866] [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_016713665.1	s__JADJOR01 sp016713665	79.3386	616	1415	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709835.1	s__UBA4427 sp002709835	78.4829	363	1415	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051925.1	s__UBA4427 sp011051925	78.3551	421	1415	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719955.1	s__UBA4427 sp002719955	77.5556	316	1415	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.5519	446	1415	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390675.1	s__UBA4427 sp002390675	76.3904	180	1415	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	99.70	99.70	0.94	0.94	2	-
GCA_018262315.1	s__PR03 sp018262315	76.3316	200	1415	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.2449	437	1415	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875225.1	s__VGRW01 sp016875225	76.1993	272	1415	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420025.1	s__Patulibacter americanus	74.9137	215	1415	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	74.8908	312	1415	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480285.1	s__GCA-2862085 sp905480285	74.8849	85	1415	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916475.1	s__Patulibacter sp017916475	74.8787	258	1415	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012718975.1	s__JAAYBF01 sp012718975	74.8762	197	1415	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Thermoleophilaceae;g__JAAYBF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:11:22,866] [INFO] GTDB search result was written to OceanDNA-b21013/result_gtdb.tsv
[2023-03-15 11:11:22,866] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:11:22,868] [INFO] DFAST_QC result json was written to OceanDNA-b21013/dqc_result.json
[2023-03-15 11:11:22,868] [INFO] DFAST_QC completed!
[2023-03-15 11:11:22,868] [INFO] Total running time: 0h2m12s