[2023-03-17 02:49:37,471] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,471] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg8028d338-56cf-471b-8cbb-b3e96301bc31/dqc_reference
[2023-03-17 02:49:38,712] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,713] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,713] [INFO] Running command: cat /var/lib/cwl/stg755b4cd5-bd89-4931-b0c1-8790a422ed02/OceanDNA-b23101.fa | prodigal -d OceanDNA-b23101/cds.fna -a OceanDNA-b23101/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:50:00,154] [INFO] Task succeeded: Prodigal
[2023-03-17 02:50:00,155] [INFO] Task started: HMMsearch
[2023-03-17 02:50:00,155] [INFO] Running command: hmmsearch --tblout OceanDNA-b23101/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8028d338-56cf-471b-8cbb-b3e96301bc31/dqc_reference/reference_markers.hmm OceanDNA-b23101/protein.faa > /dev/null
[2023-03-17 02:50:00,411] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:50:00,411] [INFO] Found 6/6 markers.
[2023-03-17 02:50:00,435] [INFO] Query marker FASTA was written to OceanDNA-b23101/markers.fasta
[2023-03-17 02:50:00,437] [INFO] Task started: Blastn
[2023-03-17 02:50:00,437] [INFO] Running command: blastn -query OceanDNA-b23101/markers.fasta -db /var/lib/cwl/stg8028d338-56cf-471b-8cbb-b3e96301bc31/dqc_reference/reference_markers.fasta -out OceanDNA-b23101/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:00,995] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:00,995] [INFO] Selected 25 target genomes.
[2023-03-17 02:50:00,996] [INFO] Target genome list was writen to OceanDNA-b23101/target_genomes.txt
[2023-03-17 02:50:01,150] [INFO] Task started: fastANI
[2023-03-17 02:50:01,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg755b4cd5-bd89-4931-b0c1-8790a422ed02/OceanDNA-b23101.fa --refList OceanDNA-b23101/target_genomes.txt --output OceanDNA-b23101/fastani_result.tsv --threads 1
[2023-03-17 02:50:20,456] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:20,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8028d338-56cf-471b-8cbb-b3e96301bc31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:50:20,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8028d338-56cf-471b-8cbb-b3e96301bc31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:50:20,469] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:50:20,469] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:50:20,469] [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
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.4193	85	1194	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.1534	104	1194	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.1232	83	1194	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.0933	119	1194	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.091	92	1194	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	74.9759	55	1194	95	below_threshold
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	74.8854	114	1194	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	74.8615	55	1194	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	74.8559	86	1194	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	74.8293	77	1194	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	74.826	104	1194	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	74.8053	93	1194	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_900104685.1	589382	589382	type	True	74.8036	93	1194	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	74.7937	97	1194	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	74.7299	103	1194	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	74.7207	117	1194	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	74.6629	112	1194	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	74.6588	113	1194	95	below_threshold
Pseudoclavibacter endophyticus	strain=EGI 60007	GCA_008831085.1	1778590	1778590	type	True	74.6447	58	1194	95	below_threshold
Pseudoclavibacter endophyticus	strain=CGMCC 1.15081	GCA_014640595.1	1778590	1778590	type	True	74.6407	59	1194	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	74.638	124	1194	95	below_threshold
Brachybacterium ginsengisoli	strain=DCY80	GCA_002407065.1	1331682	1331682	type	True	74.6334	66	1194	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:50:20,470] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23101/tc_result.tsv
[2023-03-17 02:50:20,472] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:50:20,472] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:50:20,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8028d338-56cf-471b-8cbb-b3e96301bc31/dqc_reference/checkm_data
[2023-03-17 02:50:20,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:50:20,480] [INFO] Task started: CheckM
[2023-03-17 02:50:20,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23101/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23101/checkm_input OceanDNA-b23101/checkm_result
[2023-03-17 02:51:12,896] [INFO] Task succeeded: CheckM
[2023-03-17 02:51:12,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:51:12,912] [INFO] ===== Completeness check finished =====
[2023-03-17 02:51:12,912] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:51:12,912] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23101/markers.fasta)
[2023-03-17 02:51:12,913] [INFO] Task started: Blastn
[2023-03-17 02:51:12,913] [INFO] Running command: blastn -query OceanDNA-b23101/markers.fasta -db /var/lib/cwl/stg8028d338-56cf-471b-8cbb-b3e96301bc31/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23101/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:51:13,748] [INFO] Task succeeded: Blastn
[2023-03-17 02:51:13,752] [INFO] Selected 12 target genomes.
[2023-03-17 02:51:13,752] [INFO] Target genome list was writen to OceanDNA-b23101/target_genomes_gtdb.txt
[2023-03-17 02:51:13,883] [INFO] Task started: fastANI
[2023-03-17 02:51:13,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg755b4cd5-bd89-4931-b0c1-8790a422ed02/OceanDNA-b23101.fa --refList OceanDNA-b23101/target_genomes_gtdb.txt --output OceanDNA-b23101/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:51:23,474] [INFO] Task succeeded: fastANI
[2023-03-17 02:51:23,481] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:51:23,482] [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_002684655.1	s__GCA-2684655 sp002684655	81.0903	698	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__GCA-2684655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051855.1	s__GCA-2684655 sp011051855	79.3532	447	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__GCA-2684655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794035.1	s__JAEUHS01 sp016794035	78.7257	521	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872675.1	s__UBA2386 sp016872675	78.6243	470	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794425.1	s__JAEUHS01 sp016794425	78.4629	543	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793265.1	s__UBA2386 sp016793265	78.3807	482	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793305.1	s__UBA2386 sp016793305	78.0649	417	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873195.1	s__VGXW01 sp016873195	77.9817	434	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005776475.1	s__UBA2386 sp005776475	77.3641	371	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925435.1	s__SXPK01 sp903925435	77.1074	174	1194	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__SXPK01	95.0	98.22	98.21	0.68	0.68	3	-
GCA_002862085.1	s__GCA-2862085 sp002862085	75.7335	130	1194	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_016125475.1	s__Ga0077526 sp016125475	74.6649	50	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:51:23,484] [INFO] GTDB search result was written to OceanDNA-b23101/result_gtdb.tsv
[2023-03-17 02:51:23,487] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:51:23,491] [INFO] DFAST_QC result json was written to OceanDNA-b23101/dqc_result.json
[2023-03-17 02:51:23,491] [INFO] DFAST_QC completed!
[2023-03-17 02:51:23,491] [INFO] Total running time: 0h1m46s