[2023-07-01 03:46:00,718] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:46:00,721] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:46:00,721] [INFO] DQC Reference Directory: /var/lib/cwl/stge6bc5c61-cc02-45fc-a8a7-dd8a3c79d254/dqc_reference
[2023-07-01 03:46:03,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:46:03,135] [INFO] Task started: Prodigal
[2023-07-01 03:46:03,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg71b601a4-047e-45da-8d41-41d46311be09/GCA_019233165.1_ASM1923316v1_genomic.fna.gz | prodigal -d GCA_019233165.1_ASM1923316v1_genomic.fna/cds.fna -a GCA_019233165.1_ASM1923316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:46:08,835] [INFO] Task succeeded: Prodigal
[2023-07-01 03:46:08,836] [INFO] Task started: HMMsearch
[2023-07-01 03:46:08,836] [INFO] Running command: hmmsearch --tblout GCA_019233165.1_ASM1923316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6bc5c61-cc02-45fc-a8a7-dd8a3c79d254/dqc_reference/reference_markers.hmm GCA_019233165.1_ASM1923316v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:46:09,021] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:46:09,022] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg71b601a4-047e-45da-8d41-41d46311be09/GCA_019233165.1_ASM1923316v1_genomic.fna.gz]
[2023-07-01 03:46:09,047] [INFO] Query marker FASTA was written to GCA_019233165.1_ASM1923316v1_genomic.fna/markers.fasta
[2023-07-01 03:46:09,048] [INFO] Task started: Blastn
[2023-07-01 03:46:09,048] [INFO] Running command: blastn -query GCA_019233165.1_ASM1923316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6bc5c61-cc02-45fc-a8a7-dd8a3c79d254/dqc_reference/reference_markers.fasta -out GCA_019233165.1_ASM1923316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:46:09,632] [INFO] Task succeeded: Blastn
[2023-07-01 03:46:09,636] [INFO] Selected 26 target genomes.
[2023-07-01 03:46:09,637] [INFO] Target genome list was writen to GCA_019233165.1_ASM1923316v1_genomic.fna/target_genomes.txt
[2023-07-01 03:46:09,640] [INFO] Task started: fastANI
[2023-07-01 03:46:09,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b601a4-047e-45da-8d41-41d46311be09/GCA_019233165.1_ASM1923316v1_genomic.fna.gz --refList GCA_019233165.1_ASM1923316v1_genomic.fna/target_genomes.txt --output GCA_019233165.1_ASM1923316v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:46:29,031] [INFO] Task succeeded: fastANI
[2023-07-01 03:46:29,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6bc5c61-cc02-45fc-a8a7-dd8a3c79d254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:46:29,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6bc5c61-cc02-45fc-a8a7-dd8a3c79d254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:46:29,038] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:46:29,038] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 03:46:29,039] [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
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	74.8439	53	642	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	74.6816	57	642	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	74.6636	61	642	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	74.6513	50	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 03:46:29,041] [INFO] DFAST Taxonomy check result was written to GCA_019233165.1_ASM1923316v1_genomic.fna/tc_result.tsv
[2023-07-01 03:46:29,041] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:46:29,041] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:46:29,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6bc5c61-cc02-45fc-a8a7-dd8a3c79d254/dqc_reference/checkm_data
[2023-07-01 03:46:29,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:46:29,072] [INFO] Task started: CheckM
[2023-07-01 03:46:29,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019233165.1_ASM1923316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019233165.1_ASM1923316v1_genomic.fna/checkm_input GCA_019233165.1_ASM1923316v1_genomic.fna/checkm_result
[2023-07-01 03:46:51,166] [INFO] Task succeeded: CheckM
[2023-07-01 03:46:51,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.54%
Contamintation: 8.56%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-07-01 03:46:51,184] [INFO] ===== Completeness check finished =====
[2023-07-01 03:46:51,184] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:46:51,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019233165.1_ASM1923316v1_genomic.fna/markers.fasta)
[2023-07-01 03:46:51,185] [INFO] Task started: Blastn
[2023-07-01 03:46:51,185] [INFO] Running command: blastn -query GCA_019233165.1_ASM1923316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6bc5c61-cc02-45fc-a8a7-dd8a3c79d254/dqc_reference/reference_markers_gtdb.fasta -out GCA_019233165.1_ASM1923316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:46:52,023] [INFO] Task succeeded: Blastn
[2023-07-01 03:46:52,027] [INFO] Selected 20 target genomes.
[2023-07-01 03:46:52,027] [INFO] Target genome list was writen to GCA_019233165.1_ASM1923316v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:46:52,030] [INFO] Task started: fastANI
[2023-07-01 03:46:52,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b601a4-047e-45da-8d41-41d46311be09/GCA_019233165.1_ASM1923316v1_genomic.fna.gz --refList GCA_019233165.1_ASM1923316v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019233165.1_ASM1923316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:47:02,606] [INFO] Task succeeded: fastANI
[2023-07-01 03:47:02,617] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:47:02,617] [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_019233165.1	s__JAFAMS01 sp019233165	100.0	631	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__JAFAMS01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019235885.1	s__Elarobacter sp019235885	76.5957	216	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Elarobacter	95.0	97.34	97.34	0.93	0.93	2	-
GCA_003168375.1	s__Elarobacter winogradskyi	76.5702	169	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Elarobacter	95.0	99.98	99.85	1.00	0.97	12	-
GCA_003134695.1	s__Zemynaea palustris	76.5534	113	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Zemynaea	95.0	99.68	99.42	0.94	0.92	6	-
GCA_003161435.1	s__Elarobacter pasteuri	76.5138	147	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Elarobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019233415.1	s__Elarobacter sp019233415	76.3118	134	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Elarobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151115.1	s__Rubrimentiphilum sp003151115	76.2426	65	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Rubrimentiphilum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003158195.1	s__Palsibacter borealis	76.1095	98	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Palsibacter	95.0	99.15	99.15	0.89	0.89	2	-
GCA_903970385.1	s__Palsa-1515 sp903970385	76.0964	131	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Palsa-1515	95.0	97.40	97.40	0.78	0.78	2	-
GCA_014305025.1	s__Nyctobacter psychrophilus	76.0153	71	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Nyctobacter	95.0	99.96	99.94	0.96	0.94	3	-
GCA_002413145.1	s__Zemynaea sp002413145	75.7494	80	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Zemynaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236975.1	s__JAFAHZ01 sp019236975	75.6283	62	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__JAFAHZ01	95.0	98.54	98.14	0.85	0.83	4	-
GCA_003136655.1	s__Hesperobacter lustricola	75.6266	105	642	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Hesperobacter	95.0	99.53	99.53	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-07-01 03:47:02,619] [INFO] GTDB search result was written to GCA_019233165.1_ASM1923316v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:47:02,619] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:47:02,622] [INFO] DFAST_QC result json was written to GCA_019233165.1_ASM1923316v1_genomic.fna/dqc_result.json
[2023-07-01 03:47:02,622] [INFO] DFAST_QC completed!
[2023-07-01 03:47:02,622] [INFO] Total running time: 0h1m2s