[2023-06-19 03:53:21,367] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:53:21,370] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:53:21,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg78cb0cdf-81ad-4d06-9b6c-79b844305d3d/dqc_reference
[2023-06-19 03:53:22,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:53:22,633] [INFO] Task started: Prodigal
[2023-06-19 03:53:22,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg26df37bf-38b5-41ca-a659-75842ed0aedc/GCA_013694595.1_ASM1369459v1_genomic.fna.gz | prodigal -d GCA_013694595.1_ASM1369459v1_genomic.fna/cds.fna -a GCA_013694595.1_ASM1369459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:53:41,290] [INFO] Task succeeded: Prodigal
[2023-06-19 03:53:41,290] [INFO] Task started: HMMsearch
[2023-06-19 03:53:41,290] [INFO] Running command: hmmsearch --tblout GCA_013694595.1_ASM1369459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78cb0cdf-81ad-4d06-9b6c-79b844305d3d/dqc_reference/reference_markers.hmm GCA_013694595.1_ASM1369459v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:53:41,583] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:53:41,584] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg26df37bf-38b5-41ca-a659-75842ed0aedc/GCA_013694595.1_ASM1369459v1_genomic.fna.gz]
[2023-06-19 03:53:41,617] [INFO] Query marker FASTA was written to GCA_013694595.1_ASM1369459v1_genomic.fna/markers.fasta
[2023-06-19 03:53:41,618] [INFO] Task started: Blastn
[2023-06-19 03:53:41,618] [INFO] Running command: blastn -query GCA_013694595.1_ASM1369459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78cb0cdf-81ad-4d06-9b6c-79b844305d3d/dqc_reference/reference_markers.fasta -out GCA_013694595.1_ASM1369459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:53:45,947] [INFO] Task succeeded: Blastn
[2023-06-19 03:53:45,951] [INFO] Selected 14 target genomes.
[2023-06-19 03:53:45,952] [INFO] Target genome list was writen to GCA_013694595.1_ASM1369459v1_genomic.fna/target_genomes.txt
[2023-06-19 03:53:45,957] [INFO] Task started: fastANI
[2023-06-19 03:53:45,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg26df37bf-38b5-41ca-a659-75842ed0aedc/GCA_013694595.1_ASM1369459v1_genomic.fna.gz --refList GCA_013694595.1_ASM1369459v1_genomic.fna/target_genomes.txt --output GCA_013694595.1_ASM1369459v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:53:57,542] [INFO] Task succeeded: fastANI
[2023-06-19 03:53:57,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78cb0cdf-81ad-4d06-9b6c-79b844305d3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:53:57,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78cb0cdf-81ad-4d06-9b6c-79b844305d3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:53:57,548] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:53:57,548] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 03:53:57,548] [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
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	76.1694	65	914	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	76.1304	64	914	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 03:53:57,551] [INFO] DFAST Taxonomy check result was written to GCA_013694595.1_ASM1369459v1_genomic.fna/tc_result.tsv
[2023-06-19 03:53:57,551] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:53:57,551] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:53:57,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78cb0cdf-81ad-4d06-9b6c-79b844305d3d/dqc_reference/checkm_data
[2023-06-19 03:53:57,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:53:57,593] [INFO] Task started: CheckM
[2023-06-19 03:53:57,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013694595.1_ASM1369459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013694595.1_ASM1369459v1_genomic.fna/checkm_input GCA_013694595.1_ASM1369459v1_genomic.fna/checkm_result
[2023-06-19 03:54:49,963] [INFO] Task succeeded: CheckM
[2023-06-19 03:54:49,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 10.42%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 03:54:49,991] [INFO] ===== Completeness check finished =====
[2023-06-19 03:54:49,991] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:54:49,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013694595.1_ASM1369459v1_genomic.fna/markers.fasta)
[2023-06-19 03:54:49,992] [INFO] Task started: Blastn
[2023-06-19 03:54:49,992] [INFO] Running command: blastn -query GCA_013694595.1_ASM1369459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78cb0cdf-81ad-4d06-9b6c-79b844305d3d/dqc_reference/reference_markers_gtdb.fasta -out GCA_013694595.1_ASM1369459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:54:50,929] [INFO] Task succeeded: Blastn
[2023-06-19 03:54:50,934] [INFO] Selected 17 target genomes.
[2023-06-19 03:54:50,934] [INFO] Target genome list was writen to GCA_013694595.1_ASM1369459v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:54:50,942] [INFO] Task started: fastANI
[2023-06-19 03:54:50,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg26df37bf-38b5-41ca-a659-75842ed0aedc/GCA_013694595.1_ASM1369459v1_genomic.fna.gz --refList GCA_013694595.1_ASM1369459v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013694595.1_ASM1369459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:55:00,689] [INFO] Task succeeded: fastANI
[2023-06-19 03:55:00,703] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:55:00,704] [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_013694595.1	s__JACCTI01 sp013694595	100.0	904	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__JACCTI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902805675.1	s__JACCTI01 sp902805675	78.9956	391	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__JACCTI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695905.1	s__JACCTI01 sp013695905	78.3134	238	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__JACCTI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013820755.1	s__JACCTI01 sp013820755	77.598	232	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__JACCTI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167555.1	s__AV80 sp003167555	77.2214	235	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV80	95.0	97.13	95.66	0.86	0.82	7	-
GCA_003218375.1	s__AV80 sp003218375	77.1398	207	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV80	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694945.1	s__JACCTI01 sp013694945	77.0317	106	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__JACCTI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134765.1	s__AV80 sp003134765	76.8137	183	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV80	95.0	99.94	99.85	0.97	0.93	5	-
GCA_003169975.1	s__Palsa-1392 sp003169975	76.7787	173	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Palsa-1392	95.0	99.97	99.95	0.98	0.97	5	-
GCA_013815325.1	s__Palsa-1392 sp013815325	76.7646	140	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Palsa-1392	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821455.1	s__Palsa-1392 sp013821455	76.3181	157	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Palsa-1392	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445855.1	s__UBA10450 sp003445855	75.8452	70	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__UBA10450	95.0	99.03	99.03	0.80	0.80	2	-
GCA_003219335.1	s__Udaeobacter sp003219335	75.1191	51	914	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Udaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 03:55:00,706] [INFO] GTDB search result was written to GCA_013694595.1_ASM1369459v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:55:00,706] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:55:00,709] [INFO] DFAST_QC result json was written to GCA_013694595.1_ASM1369459v1_genomic.fna/dqc_result.json
[2023-06-19 03:55:00,709] [INFO] DFAST_QC completed!
[2023-06-19 03:55:00,709] [INFO] Total running time: 0h1m39s