[2023-03-17 13:46:30,408] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:46:30,408] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:46:30,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg543cd912-19f0-403e-99e0-563ca7ca793d/dqc_reference
[2023-03-17 13:46:32,764] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:46:32,777] [INFO] Task started: Prodigal
[2023-03-17 13:46:32,777] [INFO] Running command: cat /var/lib/cwl/stg9bbded7e-6bfe-4625-be07-cc268c5ea7bd/OceanDNA-b32794.fa | prodigal -d OceanDNA-b32794/cds.fna -a OceanDNA-b32794/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:46:43,927] [INFO] Task succeeded: Prodigal
[2023-03-17 13:46:43,927] [INFO] Task started: HMMsearch
[2023-03-17 13:46:43,927] [INFO] Running command: hmmsearch --tblout OceanDNA-b32794/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg543cd912-19f0-403e-99e0-563ca7ca793d/dqc_reference/reference_markers.hmm OceanDNA-b32794/protein.faa > /dev/null
[2023-03-17 13:46:44,112] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:46:44,113] [INFO] Found 6/6 markers.
[2023-03-17 13:46:44,132] [INFO] Query marker FASTA was written to OceanDNA-b32794/markers.fasta
[2023-03-17 13:46:44,133] [INFO] Task started: Blastn
[2023-03-17 13:46:44,133] [INFO] Running command: blastn -query OceanDNA-b32794/markers.fasta -db /var/lib/cwl/stg543cd912-19f0-403e-99e0-563ca7ca793d/dqc_reference/reference_markers.fasta -out OceanDNA-b32794/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:46:44,840] [INFO] Task succeeded: Blastn
[2023-03-17 13:46:44,841] [INFO] Selected 31 target genomes.
[2023-03-17 13:46:44,841] [INFO] Target genome list was writen to OceanDNA-b32794/target_genomes.txt
[2023-03-17 13:46:44,859] [INFO] Task started: fastANI
[2023-03-17 13:46:44,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bbded7e-6bfe-4625-be07-cc268c5ea7bd/OceanDNA-b32794.fa --refList OceanDNA-b32794/target_genomes.txt --output OceanDNA-b32794/fastani_result.tsv --threads 1
[2023-03-17 13:47:22,050] [INFO] Task succeeded: fastANI
[2023-03-17 13:47:22,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg543cd912-19f0-403e-99e0-563ca7ca793d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:47:22,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg543cd912-19f0-403e-99e0-563ca7ca793d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:47:22,062] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:47:22,062] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:47:22,062] [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
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.2251	62	534	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.0649	51	534	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.0294	94	534	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.9547	70	534	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.8856	73	534	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	75.8016	60	534	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.6924	62	534	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.6504	108	534	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.6504	108	534	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.6451	57	534	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.5921	73	534	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.59	73	534	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	75.5866	55	534	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	75.585	64	534	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	75.5759	57	534	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.5073	78	534	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.4961	79	534	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.423	66	534	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	75.0945	55	534	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:47:22,062] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32794/tc_result.tsv
[2023-03-17 13:47:22,062] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:47:22,062] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:47:22,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg543cd912-19f0-403e-99e0-563ca7ca793d/dqc_reference/checkm_data
[2023-03-17 13:47:22,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:47:22,067] [INFO] Task started: CheckM
[2023-03-17 13:47:22,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32794/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32794/checkm_input OceanDNA-b32794/checkm_result
[2023-03-17 13:47:53,560] [INFO] Task succeeded: CheckM
[2023-03-17 13:47:53,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 9.38%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-17 13:47:53,563] [INFO] ===== Completeness check finished =====
[2023-03-17 13:47:53,563] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:47:53,563] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32794/markers.fasta)
[2023-03-17 13:47:53,564] [INFO] Task started: Blastn
[2023-03-17 13:47:53,564] [INFO] Running command: blastn -query OceanDNA-b32794/markers.fasta -db /var/lib/cwl/stg543cd912-19f0-403e-99e0-563ca7ca793d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32794/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:47:54,861] [INFO] Task succeeded: Blastn
[2023-03-17 13:47:54,862] [INFO] Selected 35 target genomes.
[2023-03-17 13:47:54,862] [INFO] Target genome list was writen to OceanDNA-b32794/target_genomes_gtdb.txt
[2023-03-17 13:47:55,378] [INFO] Task started: fastANI
[2023-03-17 13:47:55,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bbded7e-6bfe-4625-be07-cc268c5ea7bd/OceanDNA-b32794.fa --refList OceanDNA-b32794/target_genomes_gtdb.txt --output OceanDNA-b32794/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:48:21,094] [INFO] Task succeeded: fastANI
[2023-03-17 13:48:21,105] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:48:21,105] [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_002721365.1	s__GCA-2721365 sp002721365	76.6267	73	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2721365;f__GCA-2721365;g__GCA-2721365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.3871	57	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.2209	50	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.0294	94	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643535.1	s__Aliidongia dinghuensis	75.9547	70	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	75.912	51	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195145.1	s__JACQAF01 sp016195145	75.8657	63	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002295065.1	s__Mesorhizobium sp002295065	75.8154	53	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.6623	107	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_006739055.1	s__Stella vacuolata	75.6359	93	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124535.1	s__RI-112 sp016124535	75.6238	52	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__RI-112	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	75.5854	66	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884685.1	s__PALSA-894 sp005884685	75.5672	62	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PALSA-894	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	75.553	59	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087645.1	s__JABDJY01 sp011087645	75.5397	54	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	99.97	99.97	0.97	0.97	2	-
GCF_001305595.1	s__Azospirillum thiophilum	75.5103	78	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016185145.1	s__Reyranella sp016185145	75.4459	86	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184745.1	s__Mangrovicoccus sp013184745	75.0335	50	534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:48:21,105] [INFO] GTDB search result was written to OceanDNA-b32794/result_gtdb.tsv
[2023-03-17 13:48:21,105] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:48:21,107] [INFO] DFAST_QC result json was written to OceanDNA-b32794/dqc_result.json
[2023-03-17 13:48:21,107] [INFO] DFAST_QC completed!
[2023-03-17 13:48:21,107] [INFO] Total running time: 0h1m51s