[2023-03-18 23:44:06,351] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,351] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,351] [INFO] DQC Reference Directory: /var/lib/cwl/stg48a68b88-51da-4fcc-a09c-e4bb0a7fcd7e/dqc_reference
[2023-03-18 23:44:07,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,469] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,470] [INFO] Running command: cat /var/lib/cwl/stg42ee83c4-131b-47b1-9043-f4b5857cf5ff/OceanDNA-b41521.fa | prodigal -d OceanDNA-b41521/cds.fna -a OceanDNA-b41521/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:29,697] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:29,697] [INFO] Task started: HMMsearch
[2023-03-18 23:44:29,697] [INFO] Running command: hmmsearch --tblout OceanDNA-b41521/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48a68b88-51da-4fcc-a09c-e4bb0a7fcd7e/dqc_reference/reference_markers.hmm OceanDNA-b41521/protein.faa > /dev/null
[2023-03-18 23:44:29,915] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:29,916] [INFO] Found 6/6 markers.
[2023-03-18 23:44:29,938] [INFO] Query marker FASTA was written to OceanDNA-b41521/markers.fasta
[2023-03-18 23:44:29,939] [INFO] Task started: Blastn
[2023-03-18 23:44:29,939] [INFO] Running command: blastn -query OceanDNA-b41521/markers.fasta -db /var/lib/cwl/stg48a68b88-51da-4fcc-a09c-e4bb0a7fcd7e/dqc_reference/reference_markers.fasta -out OceanDNA-b41521/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:30,668] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:30,669] [INFO] Selected 29 target genomes.
[2023-03-18 23:44:30,669] [INFO] Target genome list was writen to OceanDNA-b41521/target_genomes.txt
[2023-03-18 23:44:30,692] [INFO] Task started: fastANI
[2023-03-18 23:44:30,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg42ee83c4-131b-47b1-9043-f4b5857cf5ff/OceanDNA-b41521.fa --refList OceanDNA-b41521/target_genomes.txt --output OceanDNA-b41521/fastani_result.tsv --threads 1
[2023-03-18 23:44:50,396] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:50,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48a68b88-51da-4fcc-a09c-e4bb0a7fcd7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:50,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48a68b88-51da-4fcc-a09c-e4bb0a7fcd7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:50,412] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:50,412] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:44:50,413] [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
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	80.863	706	1211	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.3151	136	1211	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.9965	134	1211	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.8572	105	1211	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.6768	167	1211	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.6205	149	1211	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.5269	122	1211	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	76.3421	67	1211	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	76.3421	67	1211	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	76.301	56	1211	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.2105	72	1211	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	76.2104	82	1211	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2061	99	1211	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.1974	75	1211	95	below_threshold
Pseudomonas amygdali	strain=ICMP 3918	GCA_002699855.1	47877	47877	suspected-type	True	76.1826	55	1211	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	76.1141	81	1211	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	76.104	71	1211	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	76.0705	61	1211	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.066	52	1211	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	76.0623	60	1211	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	76.0528	54	1211	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	75.9959	86	1211	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.8756	78	1211	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	75.7006	79	1211	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	75.6127	57	1211	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	75.5885	51	1211	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.4214	50	1211	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:44:50,414] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41521/tc_result.tsv
[2023-03-18 23:44:50,415] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:50,415] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:50,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48a68b88-51da-4fcc-a09c-e4bb0a7fcd7e/dqc_reference/checkm_data
[2023-03-18 23:44:50,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:50,423] [INFO] Task started: CheckM
[2023-03-18 23:44:50,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41521/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41521/checkm_input OceanDNA-b41521/checkm_result
[2023-03-18 23:45:46,178] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:46,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:46,184] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:46,185] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:46,185] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41521/markers.fasta)
[2023-03-18 23:45:46,185] [INFO] Task started: Blastn
[2023-03-18 23:45:46,185] [INFO] Running command: blastn -query OceanDNA-b41521/markers.fasta -db /var/lib/cwl/stg48a68b88-51da-4fcc-a09c-e4bb0a7fcd7e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41521/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:47,448] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:47,451] [INFO] Selected 20 target genomes.
[2023-03-18 23:45:47,451] [INFO] Target genome list was writen to OceanDNA-b41521/target_genomes_gtdb.txt
[2023-03-18 23:45:47,470] [INFO] Task started: fastANI
[2023-03-18 23:45:47,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg42ee83c4-131b-47b1-9043-f4b5857cf5ff/OceanDNA-b41521.fa --refList OceanDNA-b41521/target_genomes_gtdb.txt --output OceanDNA-b41521/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:46:00,638] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:00,649] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:46:00,649] [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_002710725.1	s__Litorivivens sp002710725	99.8064	859	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014191715.1	s__Litorivivens lipolytica	80.8586	706	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415025.1	s__Litorivivens sp002415025	78.0789	378	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	99.88	99.82	0.96	0.94	3	-
GCF_012272835.1	s__Spongiibacter sp012272835	77.0417	157	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	76.9771	135	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	76.8339	106	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.6631	168	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.4958	143	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100355.1	s__Microbulbifer yueqingensis	76.4345	91	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	76.3133	68	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	76.2228	98	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	76.2174	93	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002416125.1	s__Haliea sp002416125	76.162	97	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCF_902506505.1	s__Pseudomonas_E sp902506505	76.1015	97	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_005876855.1	s__Pseudomonas_R nosocomialis	76.0801	72	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
GCF_001045555.1	s__Marinobacter subterrani	76.0224	55	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	76.0093	77	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792665.1	s__Marinobacter orientalis	75.5915	58	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:46:00,649] [INFO] GTDB search result was written to OceanDNA-b41521/result_gtdb.tsv
[2023-03-18 23:46:00,649] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:46:00,652] [INFO] DFAST_QC result json was written to OceanDNA-b41521/dqc_result.json
[2023-03-18 23:46:00,652] [INFO] DFAST_QC completed!
[2023-03-18 23:46:00,652] [INFO] Total running time: 0h1m54s