[2023-06-19 09:52:14,182] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:52:14,188] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:52:14,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg262f577c-72d7-478e-98ef-63ce15d9ace3/dqc_reference
[2023-06-19 09:52:15,722] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:52:15,723] [INFO] Task started: Prodigal
[2023-06-19 09:52:15,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg615a63b4-bc45-45db-a4fb-eee3f96f06fb/GCA_013813865.1_ASM1381386v1_genomic.fna.gz | prodigal -d GCA_013813865.1_ASM1381386v1_genomic.fna/cds.fna -a GCA_013813865.1_ASM1381386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:52:18,947] [INFO] Task succeeded: Prodigal
[2023-06-19 09:52:18,947] [INFO] Task started: HMMsearch
[2023-06-19 09:52:18,947] [INFO] Running command: hmmsearch --tblout GCA_013813865.1_ASM1381386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg262f577c-72d7-478e-98ef-63ce15d9ace3/dqc_reference/reference_markers.hmm GCA_013813865.1_ASM1381386v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:52:19,131] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:52:19,133] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg615a63b4-bc45-45db-a4fb-eee3f96f06fb/GCA_013813865.1_ASM1381386v1_genomic.fna.gz]
[2023-06-19 09:52:19,166] [INFO] Query marker FASTA was written to GCA_013813865.1_ASM1381386v1_genomic.fna/markers.fasta
[2023-06-19 09:52:19,166] [INFO] Task started: Blastn
[2023-06-19 09:52:19,166] [INFO] Running command: blastn -query GCA_013813865.1_ASM1381386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg262f577c-72d7-478e-98ef-63ce15d9ace3/dqc_reference/reference_markers.fasta -out GCA_013813865.1_ASM1381386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:52:19,838] [INFO] Task succeeded: Blastn
[2023-06-19 09:52:19,844] [INFO] Selected 17 target genomes.
[2023-06-19 09:52:19,845] [INFO] Target genome list was writen to GCA_013813865.1_ASM1381386v1_genomic.fna/target_genomes.txt
[2023-06-19 09:52:19,849] [INFO] Task started: fastANI
[2023-06-19 09:52:19,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg615a63b4-bc45-45db-a4fb-eee3f96f06fb/GCA_013813865.1_ASM1381386v1_genomic.fna.gz --refList GCA_013813865.1_ASM1381386v1_genomic.fna/target_genomes.txt --output GCA_013813865.1_ASM1381386v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:52:32,463] [INFO] Task succeeded: fastANI
[2023-06-19 09:52:32,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg262f577c-72d7-478e-98ef-63ce15d9ace3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:52:32,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg262f577c-72d7-478e-98ef-63ce15d9ace3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:52:32,476] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:52:32,477] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:52:32,477] [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
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	79.2524	187	315	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	75.8752	138	315	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.7321	85	315	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	75.7081	88	315	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	75.7079	109	315	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.6266	105	315	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	75.4119	52	315	95	below_threshold
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	75.1135	59	315	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	75.0611	64	315	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.9717	51	315	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	74.8544	54	315	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	74.8463	55	315	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	74.8047	64	315	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:52:32,479] [INFO] DFAST Taxonomy check result was written to GCA_013813865.1_ASM1381386v1_genomic.fna/tc_result.tsv
[2023-06-19 09:52:32,480] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:52:32,480] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:52:32,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg262f577c-72d7-478e-98ef-63ce15d9ace3/dqc_reference/checkm_data
[2023-06-19 09:52:32,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:52:32,504] [INFO] Task started: CheckM
[2023-06-19 09:52:32,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013813865.1_ASM1381386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013813865.1_ASM1381386v1_genomic.fna/checkm_input GCA_013813865.1_ASM1381386v1_genomic.fna/checkm_result
[2023-06-19 09:52:50,409] [INFO] Task succeeded: CheckM
[2023-06-19 09:52:50,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.38%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 09:52:50,438] [INFO] ===== Completeness check finished =====
[2023-06-19 09:52:50,439] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:52:50,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013813865.1_ASM1381386v1_genomic.fna/markers.fasta)
[2023-06-19 09:52:50,440] [INFO] Task started: Blastn
[2023-06-19 09:52:50,440] [INFO] Running command: blastn -query GCA_013813865.1_ASM1381386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg262f577c-72d7-478e-98ef-63ce15d9ace3/dqc_reference/reference_markers_gtdb.fasta -out GCA_013813865.1_ASM1381386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:52:51,473] [INFO] Task succeeded: Blastn
[2023-06-19 09:52:51,477] [INFO] Selected 13 target genomes.
[2023-06-19 09:52:51,477] [INFO] Target genome list was writen to GCA_013813865.1_ASM1381386v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:52:51,483] [INFO] Task started: fastANI
[2023-06-19 09:52:51,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg615a63b4-bc45-45db-a4fb-eee3f96f06fb/GCA_013813865.1_ASM1381386v1_genomic.fna.gz --refList GCA_013813865.1_ASM1381386v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013813865.1_ASM1381386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:52:56,894] [INFO] Task succeeded: fastANI
[2023-06-19 09:52:56,906] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 09:52:56,907] [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_013813345.1	s__JACCRW01 sp013813345	80.3902	172	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351045.1	s__Gaiella occulta	79.2516	187	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Gaiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884575.1	s__AC-16 sp005884575	79.0113	179	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236545.1	s__Palsa-739 sp019236545	78.8784	152	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	98.19	98.19	0.82	0.82	2	-
GCA_903930195.1	s__PALSA-600 sp903930195	78.6012	100	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__PALSA-600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812235.1	s__JACCTU01 sp013812235	78.5162	103	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883965.1	s__AC-32 sp005883965	78.4721	132	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883335.1	s__AC-32 sp005883335	78.4216	114	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884155.1	s__AC-32 sp005884155	78.3041	122	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696185.1	s__JACCZA01 sp013696185	78.2726	155	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCZA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139545.1	s__Palsa-739 sp003139545	78.2565	162	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870235.1	s__Gaiella sp016870235	78.0857	125	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Gaiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014534295.1	s__JACVRU01 sp014534295	77.581	91	315	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACVRU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 09:52:56,909] [INFO] GTDB search result was written to GCA_013813865.1_ASM1381386v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:52:56,910] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:52:56,914] [INFO] DFAST_QC result json was written to GCA_013813865.1_ASM1381386v1_genomic.fna/dqc_result.json
[2023-06-19 09:52:56,914] [INFO] DFAST_QC completed!
[2023-06-19 09:52:56,914] [INFO] Total running time: 0h0m43s