[2023-03-16 09:50:49,913] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:50:49,920] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:50:49,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg59d8a102-2518-4282-8df2-ed998fc9ca92/dqc_reference
[2023-03-16 09:50:51,016] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:50:51,016] [INFO] Task started: Prodigal
[2023-03-16 09:50:51,016] [INFO] Running command: cat /var/lib/cwl/stg7dc66501-84df-484c-91ce-432985821acf/OceanDNA-b23015.fa | prodigal -d OceanDNA-b23015/cds.fna -a OceanDNA-b23015/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:51:29,005] [INFO] Task succeeded: Prodigal
[2023-03-16 09:51:29,005] [INFO] Task started: HMMsearch
[2023-03-16 09:51:29,005] [INFO] Running command: hmmsearch --tblout OceanDNA-b23015/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59d8a102-2518-4282-8df2-ed998fc9ca92/dqc_reference/reference_markers.hmm OceanDNA-b23015/protein.faa > /dev/null
[2023-03-16 09:51:29,268] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:51:29,269] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7dc66501-84df-484c-91ce-432985821acf/OceanDNA-b23015.fa]
[2023-03-16 09:51:29,321] [INFO] Query marker FASTA was written to OceanDNA-b23015/markers.fasta
[2023-03-16 09:51:29,323] [INFO] Task started: Blastn
[2023-03-16 09:51:29,323] [INFO] Running command: blastn -query OceanDNA-b23015/markers.fasta -db /var/lib/cwl/stg59d8a102-2518-4282-8df2-ed998fc9ca92/dqc_reference/reference_markers.fasta -out OceanDNA-b23015/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:51:30,009] [INFO] Task succeeded: Blastn
[2023-03-16 09:51:30,017] [INFO] Selected 24 target genomes.
[2023-03-16 09:51:30,017] [INFO] Target genome list was writen to OceanDNA-b23015/target_genomes.txt
[2023-03-16 09:51:30,059] [INFO] Task started: fastANI
[2023-03-16 09:51:30,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dc66501-84df-484c-91ce-432985821acf/OceanDNA-b23015.fa --refList OceanDNA-b23015/target_genomes.txt --output OceanDNA-b23015/fastani_result.tsv --threads 1
[2023-03-16 09:51:49,757] [INFO] Task succeeded: fastANI
[2023-03-16 09:51:49,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59d8a102-2518-4282-8df2-ed998fc9ca92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:51:49,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59d8a102-2518-4282-8df2-ed998fc9ca92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:51:49,771] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:51:49,771] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:51:49,771] [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
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	74.9931	81	2080	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	74.976	135	2080	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	74.9361	52	2080	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8715	224	2080	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.8641	455	2080	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	74.8452	162	2080	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	74.8367	103	2080	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.8257	158	2080	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	74.8184	143	2080	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	74.7926	107	2080	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.7816	257	2080	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	74.7759	259	2080	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	74.7693	196	2080	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	74.7608	148	2080	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	74.758	195	2080	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	74.7484	158	2080	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	74.7475	159	2080	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	74.7453	161	2080	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	74.7033	76	2080	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	74.6613	145	2080	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	74.6405	115	2080	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	74.6318	87	2080	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	74.6307	86	2080	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:51:49,775] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23015/tc_result.tsv
[2023-03-16 09:51:49,777] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:51:49,777] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:51:49,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59d8a102-2518-4282-8df2-ed998fc9ca92/dqc_reference/checkm_data
[2023-03-16 09:51:49,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:51:49,789] [INFO] Task started: CheckM
[2023-03-16 09:51:49,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23015/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23015/checkm_input OceanDNA-b23015/checkm_result
[2023-03-16 09:53:23,167] [INFO] Task succeeded: CheckM
[2023-03-16 09:53:23,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:53:23,204] [INFO] ===== Completeness check finished =====
[2023-03-16 09:53:23,204] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:53:23,205] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23015/markers.fasta)
[2023-03-16 09:53:23,206] [INFO] Task started: Blastn
[2023-03-16 09:53:23,206] [INFO] Running command: blastn -query OceanDNA-b23015/markers.fasta -db /var/lib/cwl/stg59d8a102-2518-4282-8df2-ed998fc9ca92/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23015/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:53:24,419] [INFO] Task succeeded: Blastn
[2023-03-16 09:53:24,428] [INFO] Selected 22 target genomes.
[2023-03-16 09:53:24,428] [INFO] Target genome list was writen to OceanDNA-b23015/target_genomes_gtdb.txt
[2023-03-16 09:53:24,477] [INFO] Task started: fastANI
[2023-03-16 09:53:24,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dc66501-84df-484c-91ce-432985821acf/OceanDNA-b23015.fa --refList OceanDNA-b23015/target_genomes_gtdb.txt --output OceanDNA-b23015/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:53:41,816] [INFO] Task succeeded: fastANI
[2023-03-16 09:53:41,827] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:53:41,827] [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_007750655.1	s__Pla163 sp007750655	76.6976	305	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751255.1	s__Pla86 sp007751255	76.5807	446	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla86	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009691855.1	s__JABFRZ01 sp009691855	76.5573	383	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712565.1	s__JADJQU01 sp016712565	76.5344	333	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJQU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140785.1	s__JABFRZ01 sp013140785	76.5148	271	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892045.1	s__F1-120-MAGs118 sp903892045	76.4491	351	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.41	99.41	0.87	0.87	3	-
GCA_002686265.1	s__GCA-2686265 sp002686265	76.4186	284	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	76.401	274	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928115.1	s__F1-120-MAGs118 sp903928115	76.3857	253	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.83	99.80	0.95	0.95	3	-
GCA_902826945.1	s__RBC036 sp902826945	76.3279	518	2080	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_011053145.1	s__DRLC01 sp011053145	76.1872	195	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__DRLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959525.1	s__GCA-2720975 sp012959525	76.177	118	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2720975	95.0	99.90	99.90	0.93	0.93	2	-
GCA_011525785.1	s__WYBT01 sp011525785	76.048	484	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	75.9047	296	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795325.1	s__WYBT01 sp016795325	75.8959	408	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862085.1	s__GCA-2862085 sp002862085	75.8241	248	2080	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	-
GCA_007751475.1	s__GCA-2862085 sp007751475	75.7678	240	2080	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	-
GCA_016714045.1	s__JADJNY01 sp016714045	75.6055	424	2080	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001750625.1	s__AqS2 sp001750625	74.8652	66	2080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__AqS2;f__AqS2;g__AqS2	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100455.1	s__Roseospirillum parvum	74.8256	106	2080	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:53:41,831] [INFO] GTDB search result was written to OceanDNA-b23015/result_gtdb.tsv
[2023-03-16 09:53:41,837] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:53:41,841] [INFO] DFAST_QC result json was written to OceanDNA-b23015/dqc_result.json
[2023-03-16 09:53:41,841] [INFO] DFAST_QC completed!
[2023-03-16 09:53:41,841] [INFO] Total running time: 0h2m52s