[2023-06-30 09:59:39,767] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:59:39,785] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:59:39,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg7970489f-9b0f-4312-97b3-44ecd8fa55ab/dqc_reference
[2023-06-30 09:59:41,194] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:59:41,194] [INFO] Task started: Prodigal
[2023-06-30 09:59:41,195] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e810fbb-8ec0-4e9a-9fc8-cd27b005a77a/GCA_016721085.1_ASM1672108v1_genomic.fna.gz | prodigal -d GCA_016721085.1_ASM1672108v1_genomic.fna/cds.fna -a GCA_016721085.1_ASM1672108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:00:03,403] [INFO] Task succeeded: Prodigal
[2023-06-30 10:00:03,403] [INFO] Task started: HMMsearch
[2023-06-30 10:00:03,403] [INFO] Running command: hmmsearch --tblout GCA_016721085.1_ASM1672108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7970489f-9b0f-4312-97b3-44ecd8fa55ab/dqc_reference/reference_markers.hmm GCA_016721085.1_ASM1672108v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:00:03,703] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:00:03,705] [INFO] Found 6/6 markers.
[2023-06-30 10:00:03,749] [INFO] Query marker FASTA was written to GCA_016721085.1_ASM1672108v1_genomic.fna/markers.fasta
[2023-06-30 10:00:03,750] [INFO] Task started: Blastn
[2023-06-30 10:00:03,750] [INFO] Running command: blastn -query GCA_016721085.1_ASM1672108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7970489f-9b0f-4312-97b3-44ecd8fa55ab/dqc_reference/reference_markers.fasta -out GCA_016721085.1_ASM1672108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:00:04,368] [INFO] Task succeeded: Blastn
[2023-06-30 10:00:04,381] [INFO] Selected 28 target genomes.
[2023-06-30 10:00:04,382] [INFO] Target genome list was writen to GCA_016721085.1_ASM1672108v1_genomic.fna/target_genomes.txt
[2023-06-30 10:00:04,384] [INFO] Task started: fastANI
[2023-06-30 10:00:04,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e810fbb-8ec0-4e9a-9fc8-cd27b005a77a/GCA_016721085.1_ASM1672108v1_genomic.fna.gz --refList GCA_016721085.1_ASM1672108v1_genomic.fna/target_genomes.txt --output GCA_016721085.1_ASM1672108v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:00:30,041] [INFO] Task succeeded: fastANI
[2023-06-30 10:00:30,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7970489f-9b0f-4312-97b3-44ecd8fa55ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:00:30,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7970489f-9b0f-4312-97b3-44ecd8fa55ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:00:30,055] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:00:30,055] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:00:30,055] [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
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.934	53	1747	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	76.7275	117	1747	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.6915	102	1747	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.4816	97	1747	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	76.3816	101	1747	95	below_threshold
Flavihumibacter profundi	strain=KCTC 62290	GCA_020076305.1	2716883	2716883	type	True	76.3612	84	1747	95	below_threshold
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	76.3519	55	1747	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.3434	127	1747	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	76.328	98	1747	95	below_threshold
Terrimonas ferruginea	strain=DSM 30193	GCA_000425585.1	249	249	type	True	76.2732	71	1747	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.2567	95	1747	95	below_threshold
Flavisolibacter ginsengisoli	strain=DSM 18119	GCA_900129295.1	462367	462367	type	True	76.1695	68	1747	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	75.4128	50	1747	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:00:30,057] [INFO] DFAST Taxonomy check result was written to GCA_016721085.1_ASM1672108v1_genomic.fna/tc_result.tsv
[2023-06-30 10:00:30,058] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:00:30,058] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:00:30,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7970489f-9b0f-4312-97b3-44ecd8fa55ab/dqc_reference/checkm_data
[2023-06-30 10:00:30,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:00:30,112] [INFO] Task started: CheckM
[2023-06-30 10:00:30,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016721085.1_ASM1672108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016721085.1_ASM1672108v1_genomic.fna/checkm_input GCA_016721085.1_ASM1672108v1_genomic.fna/checkm_result
[2023-06-30 10:01:32,789] [INFO] Task succeeded: CheckM
[2023-06-30 10:01:32,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:01:32,816] [INFO] ===== Completeness check finished =====
[2023-06-30 10:01:32,816] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:01:32,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016721085.1_ASM1672108v1_genomic.fna/markers.fasta)
[2023-06-30 10:01:32,817] [INFO] Task started: Blastn
[2023-06-30 10:01:32,817] [INFO] Running command: blastn -query GCA_016721085.1_ASM1672108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7970489f-9b0f-4312-97b3-44ecd8fa55ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_016721085.1_ASM1672108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:01:33,629] [INFO] Task succeeded: Blastn
[2023-06-30 10:01:33,634] [INFO] Selected 24 target genomes.
[2023-06-30 10:01:33,635] [INFO] Target genome list was writen to GCA_016721085.1_ASM1672108v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:01:33,637] [INFO] Task started: fastANI
[2023-06-30 10:01:33,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e810fbb-8ec0-4e9a-9fc8-cd27b005a77a/GCA_016721085.1_ASM1672108v1_genomic.fna.gz --refList GCA_016721085.1_ASM1672108v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016721085.1_ASM1672108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:01:52,097] [INFO] Task succeeded: fastANI
[2023-06-30 10:01:52,116] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:01:52,116] [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_016721085.1	s__UBA3961 sp016721085	99.9999	1742	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA3961	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012927185.1	s__Pseudobacter sp012927185	76.7454	83	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970185.1	s__Pseudobacter ginsenosidimutans	76.6902	101	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011357845.1	s__UBA3961 sp011357845	76.6018	185	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA3961	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706055.1	s__JJ008 sp016706055	76.5317	68	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.30	99.30	0.94	0.94	2	-
GCA_002337125.1	s__Lacibacter sp002337125	76.413	79	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759375.1	s__Paraflavitalea devenefica	76.3434	127	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744515.1	s__Paraflavitalea sp017744515	76.3341	110	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306865.1	s__JAFKHH01 sp017306865	76.2792	61	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFKHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963365.1	s__AWTP1-9 sp003963365	76.2655	101	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129295.1	s__Flavisolibacter ginsengisoli	76.0892	60	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719165.1	s__JJ008 sp016719165	75.9866	72	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.96	97.46	0.92	0.92	3	-
GCA_003243445.1	s__46-32 sp003243445	75.8778	75	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141115.1	s__Ferruginibacter sp013141115	75.8632	61	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786885.1	s__JJ008 sp016786885	75.8392	65	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331705.1	s__JJ008 sp011331705	75.7783	53	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303455.1	s__JJ008 sp017303455	75.7753	86	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352145.1	s__JJ008 sp002352145	75.5735	61	1747	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:01:52,119] [INFO] GTDB search result was written to GCA_016721085.1_ASM1672108v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:01:52,119] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:01:52,124] [INFO] DFAST_QC result json was written to GCA_016721085.1_ASM1672108v1_genomic.fna/dqc_result.json
[2023-06-30 10:01:52,124] [INFO] DFAST_QC completed!
[2023-06-30 10:01:52,124] [INFO] Total running time: 0h2m12s