[2023-03-16 20:07:31,832] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:07:31,832] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:07:31,833] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f022cab-8d1d-4086-ae8b-ed40b3a633c7/dqc_reference
[2023-03-16 20:07:32,954] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:07:32,954] [INFO] Task started: Prodigal
[2023-03-16 20:07:32,954] [INFO] Running command: cat /var/lib/cwl/stgee65def2-7296-4988-aa62-781fb4081378/OceanDNA-b20907.fa | prodigal -d OceanDNA-b20907/cds.fna -a OceanDNA-b20907/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:08:03,727] [INFO] Task succeeded: Prodigal
[2023-03-16 20:08:03,727] [INFO] Task started: HMMsearch
[2023-03-16 20:08:03,727] [INFO] Running command: hmmsearch --tblout OceanDNA-b20907/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f022cab-8d1d-4086-ae8b-ed40b3a633c7/dqc_reference/reference_markers.hmm OceanDNA-b20907/protein.faa > /dev/null
[2023-03-16 20:08:03,964] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:08:03,965] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgee65def2-7296-4988-aa62-781fb4081378/OceanDNA-b20907.fa]
[2023-03-16 20:08:03,999] [INFO] Query marker FASTA was written to OceanDNA-b20907/markers.fasta
[2023-03-16 20:08:04,000] [INFO] Task started: Blastn
[2023-03-16 20:08:04,000] [INFO] Running command: blastn -query OceanDNA-b20907/markers.fasta -db /var/lib/cwl/stg7f022cab-8d1d-4086-ae8b-ed40b3a633c7/dqc_reference/reference_markers.fasta -out OceanDNA-b20907/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:08:04,654] [INFO] Task succeeded: Blastn
[2023-03-16 20:08:04,655] [INFO] Selected 27 target genomes.
[2023-03-16 20:08:04,656] [INFO] Target genome list was writen to OceanDNA-b20907/target_genomes.txt
[2023-03-16 20:08:04,668] [INFO] Task started: fastANI
[2023-03-16 20:08:04,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgee65def2-7296-4988-aa62-781fb4081378/OceanDNA-b20907.fa --refList OceanDNA-b20907/target_genomes.txt --output OceanDNA-b20907/fastani_result.tsv --threads 1
[2023-03-16 20:08:24,495] [INFO] Task succeeded: fastANI
[2023-03-16 20:08:24,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f022cab-8d1d-4086-ae8b-ed40b3a633c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:08:24,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f022cab-8d1d-4086-ae8b-ed40b3a633c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:08:24,509] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:08:24,509] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:08:24,509] [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
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	76.5024	438	1678	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.7572	395	1678	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.742	397	1678	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	75.0277	60	1678	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	75.0254	80	1678	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	75.0211	80	1678	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.9999	217	1678	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	74.9081	92	1678	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	74.8976	94	1678	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	74.8052	73	1678	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	74.7825	85	1678	95	below_threshold
Agromyces salentinus	strain=JCM 14323	GCA_009749395.1	269421	269421	type	True	74.7768	87	1678	95	below_threshold
Lysobacter xinjiangensis	strain=KCTC 22558	GCA_014651995.1	546892	546892	type	True	74.7715	62	1678	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	74.7202	97	1678	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.7198	80	1678	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	74.7147	83	1678	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	74.7004	77	1678	95	below_threshold
Lysobacter bugurensis	strain=KCTC 23077	GCA_014652095.1	543356	543356	type	True	74.6926	59	1678	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.6819	92	1678	95	below_threshold
Jatrophihabitans endophyticus	strain=DSM 45627	GCA_900129455.1	1206085	1206085	type	True	74.6504	101	1678	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	74.6351	69	1678	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	74.6347	72	1678	95	below_threshold
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	74.6065	61	1678	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:08:24,509] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20907/tc_result.tsv
[2023-03-16 20:08:24,509] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:08:24,509] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:08:24,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f022cab-8d1d-4086-ae8b-ed40b3a633c7/dqc_reference/checkm_data
[2023-03-16 20:08:24,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:08:24,616] [INFO] Task started: CheckM
[2023-03-16 20:08:24,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20907/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20907/checkm_input OceanDNA-b20907/checkm_result
[2023-03-16 20:09:58,823] [INFO] Task succeeded: CheckM
[2023-03-16 20:09:58,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:09:58,828] [INFO] ===== Completeness check finished =====
[2023-03-16 20:09:58,828] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:09:58,829] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20907/markers.fasta)
[2023-03-16 20:09:58,830] [INFO] Task started: Blastn
[2023-03-16 20:09:58,830] [INFO] Running command: blastn -query OceanDNA-b20907/markers.fasta -db /var/lib/cwl/stg7f022cab-8d1d-4086-ae8b-ed40b3a633c7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20907/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:09:59,997] [INFO] Task succeeded: Blastn
[2023-03-16 20:09:59,998] [INFO] Selected 24 target genomes.
[2023-03-16 20:09:59,998] [INFO] Target genome list was writen to OceanDNA-b20907/target_genomes_gtdb.txt
[2023-03-16 20:10:00,042] [INFO] Task started: fastANI
[2023-03-16 20:10:00,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgee65def2-7296-4988-aa62-781fb4081378/OceanDNA-b20907.fa --refList OceanDNA-b20907/target_genomes_gtdb.txt --output OceanDNA-b20907/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:10:23,774] [INFO] Task succeeded: fastANI
[2023-03-16 20:10:23,785] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 20:10:23,785] [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_000170895.1	s__Plesiocystis pacifica	76.5195	433	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240065.1	s__JAAZXR01 sp014240065	76.3662	143	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JAAZXR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994615.1	s__Enhygromyxa salina_A	76.3357	411	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737335.2	s__Enhygromyxa salina_C	76.17	350	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812955.1	s__Nannocystis sp013812955	76.0982	225	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994635.1	s__Enhygromyxa salina_B	76.0877	386	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	75.8034	328	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCF_002343915.1	s__Nannocystis exedens	75.7527	394	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016714285.1	s__Nannocystis sp016714285	75.691	312	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCA_001464385.1	s__Ga0077550 sp001464385	75.6798	357	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712315.1	s__JADJRG01 sp016712315	75.5227	234	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826865.1	s__Ga0077550 sp902826865	75.3396	150	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696105.1	s__J016 sp003696105	74.868	139	1678	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__J016;g__J016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	74.7885	77	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017993425.1	s__Amaricoccus sp017993425	74.7673	85	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	74.6963	78	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	74.6703	100	1678	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000603945.1	s__Actinotalea ferrariae	74.6197	58	1678	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789225.1	s__WSTA01 sp009789225	74.6099	109	1678	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 20:10:23,786] [INFO] GTDB search result was written to OceanDNA-b20907/result_gtdb.tsv
[2023-03-16 20:10:23,787] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:10:23,790] [INFO] DFAST_QC result json was written to OceanDNA-b20907/dqc_result.json
[2023-03-16 20:10:23,790] [INFO] DFAST_QC completed!
[2023-03-16 20:10:23,790] [INFO] Total running time: 0h2m52s