[2023-06-29 23:16:08,456] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:16:08,458] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:16:08,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg8868aded-9146-4bf8-96ae-53c11a0fef9c/dqc_reference
[2023-06-29 23:16:09,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:16:09,683] [INFO] Task started: Prodigal
[2023-06-29 23:16:09,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d7919f5-324d-427b-97cb-3268f471fa0b/GCA_016708565.1_ASM1670856v1_genomic.fna.gz | prodigal -d GCA_016708565.1_ASM1670856v1_genomic.fna/cds.fna -a GCA_016708565.1_ASM1670856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:16:36,653] [INFO] Task succeeded: Prodigal
[2023-06-29 23:16:36,653] [INFO] Task started: HMMsearch
[2023-06-29 23:16:36,653] [INFO] Running command: hmmsearch --tblout GCA_016708565.1_ASM1670856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8868aded-9146-4bf8-96ae-53c11a0fef9c/dqc_reference/reference_markers.hmm GCA_016708565.1_ASM1670856v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:16:37,114] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:16:37,116] [INFO] Found 6/6 markers.
[2023-06-29 23:16:37,197] [INFO] Query marker FASTA was written to GCA_016708565.1_ASM1670856v1_genomic.fna/markers.fasta
[2023-06-29 23:16:37,198] [INFO] Task started: Blastn
[2023-06-29 23:16:37,198] [INFO] Running command: blastn -query GCA_016708565.1_ASM1670856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8868aded-9146-4bf8-96ae-53c11a0fef9c/dqc_reference/reference_markers.fasta -out GCA_016708565.1_ASM1670856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:16:38,174] [INFO] Task succeeded: Blastn
[2023-06-29 23:16:38,178] [INFO] Selected 35 target genomes.
[2023-06-29 23:16:38,179] [INFO] Target genome list was writen to GCA_016708565.1_ASM1670856v1_genomic.fna/target_genomes.txt
[2023-06-29 23:16:38,180] [INFO] Task started: fastANI
[2023-06-29 23:16:38,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d7919f5-324d-427b-97cb-3268f471fa0b/GCA_016708565.1_ASM1670856v1_genomic.fna.gz --refList GCA_016708565.1_ASM1670856v1_genomic.fna/target_genomes.txt --output GCA_016708565.1_ASM1670856v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:17:29,762] [INFO] Task succeeded: fastANI
[2023-06-29 23:17:29,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8868aded-9146-4bf8-96ae-53c11a0fef9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:17:29,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8868aded-9146-4bf8-96ae-53c11a0fef9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:17:29,788] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:17:29,788] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:17:29,788] [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
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	76.4026	1158	3367	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.5183	854	3367	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.3929	1394	3367	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.3677	1254	3367	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.3494	1386	3367	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	75.3448	168	3367	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	75.2778	420	3367	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	75.2405	896	3367	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	75.2396	177	3367	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	75.2326	236	3367	95	below_threshold
Geomonas ferrireducens	strain=S62	GCA_004917065.1	2570227	2570227	type	True	75.2232	131	3367	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	75.218	232	3367	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	75.2168	147	3367	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.2135	425	3367	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	75.1931	506	3367	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	75.189	588	3367	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.1654	389	3367	95	below_threshold
Pseudoxanthomonas dokdonensis	strain=DSM 21858	GCA_001431405.1	344882	344882	type	True	75.1248	200	3367	95	below_threshold
Aquabacterium parvum	strain=B6	GCA_001447195.1	70584	70584	type	True	75.1189	200	3367	95	below_threshold
Wenzhouxiangella sediminis	strain=XDB06	GCA_003410055.1	1792836	1792836	type	True	75.1174	222	3367	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	75.104	560	3367	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	75.1001	409	3367	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	75.0627	612	3367	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	75.0164	624	3367	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	74.9957	466	3367	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	74.9632	987	3367	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	74.9493	954	3367	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	74.9358	806	3367	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	74.9155	857	3367	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	74.8894	718	3367	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	74.8647	790	3367	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	74.8516	578	3367	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	74.6527	280	3367	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	74.6462	207	3367	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:17:29,790] [INFO] DFAST Taxonomy check result was written to GCA_016708565.1_ASM1670856v1_genomic.fna/tc_result.tsv
[2023-06-29 23:17:29,791] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:17:29,792] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:17:29,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8868aded-9146-4bf8-96ae-53c11a0fef9c/dqc_reference/checkm_data
[2023-06-29 23:17:29,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:17:29,893] [INFO] Task started: CheckM
[2023-06-29 23:17:29,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708565.1_ASM1670856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708565.1_ASM1670856v1_genomic.fna/checkm_input GCA_016708565.1_ASM1670856v1_genomic.fna/checkm_result
[2023-06-29 23:19:15,451] [INFO] Task succeeded: CheckM
[2023-06-29 23:19:15,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 23:19:15,484] [INFO] ===== Completeness check finished =====
[2023-06-29 23:19:15,484] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:19:15,485] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708565.1_ASM1670856v1_genomic.fna/markers.fasta)
[2023-06-29 23:19:15,485] [INFO] Task started: Blastn
[2023-06-29 23:19:15,485] [INFO] Running command: blastn -query GCA_016708565.1_ASM1670856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8868aded-9146-4bf8-96ae-53c11a0fef9c/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708565.1_ASM1670856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:19:17,173] [INFO] Task succeeded: Blastn
[2023-06-29 23:19:17,178] [INFO] Selected 9 target genomes.
[2023-06-29 23:19:17,178] [INFO] Target genome list was writen to GCA_016708565.1_ASM1670856v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:19:17,180] [INFO] Task started: fastANI
[2023-06-29 23:19:17,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d7919f5-324d-427b-97cb-3268f471fa0b/GCA_016708565.1_ASM1670856v1_genomic.fna.gz --refList GCA_016708565.1_ASM1670856v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708565.1_ASM1670856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:20:09,776] [INFO] Task succeeded: fastANI
[2023-06-29 23:20:09,790] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:20:09,791] [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_016707895.1	s__UBA2376 sp016707895	99.6087	3113	3367	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	conclusive
GCA_016794525.1	s__UBA2376 sp016794525	93.717	2678	3367	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	86.1991	2294	3367	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057825.1	s__UBA2376 sp018057825	83.1157	1975	3367	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.99	99.98	0.98	0.98	3	-
GCA_900696455.1	s__UBA2376 sp900696455	80.7132	1598	3367	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_002344285.1	s__UBA2376 sp002344285	79.3819	1593	3367	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005779305.1	s__UBA2376 sp005779305	79.1422	1470	3367	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526095.1	s__WYBA01 sp011526095	79.1235	1698	3367	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058095.1	s__JABFXX01 sp018058095	78.4646	1506	3367	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	99.29	99.24	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-29 23:20:09,793] [INFO] GTDB search result was written to GCA_016708565.1_ASM1670856v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:20:09,794] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:20:09,799] [INFO] DFAST_QC result json was written to GCA_016708565.1_ASM1670856v1_genomic.fna/dqc_result.json
[2023-06-29 23:20:09,799] [INFO] DFAST_QC completed!
[2023-06-29 23:20:09,799] [INFO] Total running time: 0h4m1s