[2023-06-29 03:05:46,201] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:05:46,203] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:05:46,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg965bdd12-f1c8-46ec-b597-ccd03e6647fe/dqc_reference
[2023-06-29 03:05:47,416] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:05:47,418] [INFO] Task started: Prodigal
[2023-06-29 03:05:47,418] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b03ccde-13ea-4d31-8508-5f79f7c6b380/GCA_027039925.1_ASM2703992v1_genomic.fna.gz | prodigal -d GCA_027039925.1_ASM2703992v1_genomic.fna/cds.fna -a GCA_027039925.1_ASM2703992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:05:57,898] [INFO] Task succeeded: Prodigal
[2023-06-29 03:05:57,898] [INFO] Task started: HMMsearch
[2023-06-29 03:05:57,898] [INFO] Running command: hmmsearch --tblout GCA_027039925.1_ASM2703992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg965bdd12-f1c8-46ec-b597-ccd03e6647fe/dqc_reference/reference_markers.hmm GCA_027039925.1_ASM2703992v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:05:58,184] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:05:58,185] [INFO] Found 6/6 markers.
[2023-06-29 03:05:58,225] [INFO] Query marker FASTA was written to GCA_027039925.1_ASM2703992v1_genomic.fna/markers.fasta
[2023-06-29 03:05:58,225] [INFO] Task started: Blastn
[2023-06-29 03:05:58,225] [INFO] Running command: blastn -query GCA_027039925.1_ASM2703992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg965bdd12-f1c8-46ec-b597-ccd03e6647fe/dqc_reference/reference_markers.fasta -out GCA_027039925.1_ASM2703992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:05:58,890] [INFO] Task succeeded: Blastn
[2023-06-29 03:05:58,897] [INFO] Selected 23 target genomes.
[2023-06-29 03:05:58,898] [INFO] Target genome list was writen to GCA_027039925.1_ASM2703992v1_genomic.fna/target_genomes.txt
[2023-06-29 03:05:58,904] [INFO] Task started: fastANI
[2023-06-29 03:05:58,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b03ccde-13ea-4d31-8508-5f79f7c6b380/GCA_027039925.1_ASM2703992v1_genomic.fna.gz --refList GCA_027039925.1_ASM2703992v1_genomic.fna/target_genomes.txt --output GCA_027039925.1_ASM2703992v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:06:16,693] [INFO] Task succeeded: fastANI
[2023-06-29 03:06:16,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg965bdd12-f1c8-46ec-b597-ccd03e6647fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:06:16,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg965bdd12-f1c8-46ec-b597-ccd03e6647fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:06:16,697] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:06:16,698] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:06:16,698] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	75.9825	65	1116	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:06:16,700] [INFO] DFAST Taxonomy check result was written to GCA_027039925.1_ASM2703992v1_genomic.fna/tc_result.tsv
[2023-06-29 03:06:16,700] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:06:16,700] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:06:16,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg965bdd12-f1c8-46ec-b597-ccd03e6647fe/dqc_reference/checkm_data
[2023-06-29 03:06:16,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:06:16,747] [INFO] Task started: CheckM
[2023-06-29 03:06:16,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027039925.1_ASM2703992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027039925.1_ASM2703992v1_genomic.fna/checkm_input GCA_027039925.1_ASM2703992v1_genomic.fna/checkm_result
[2023-06-29 03:06:51,579] [INFO] Task succeeded: CheckM
[2023-06-29 03:06:51,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:06:51,603] [INFO] ===== Completeness check finished =====
[2023-06-29 03:06:51,603] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:06:51,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027039925.1_ASM2703992v1_genomic.fna/markers.fasta)
[2023-06-29 03:06:51,604] [INFO] Task started: Blastn
[2023-06-29 03:06:51,604] [INFO] Running command: blastn -query GCA_027039925.1_ASM2703992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg965bdd12-f1c8-46ec-b597-ccd03e6647fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_027039925.1_ASM2703992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:06:52,496] [INFO] Task succeeded: Blastn
[2023-06-29 03:06:52,501] [INFO] Selected 18 target genomes.
[2023-06-29 03:06:52,501] [INFO] Target genome list was writen to GCA_027039925.1_ASM2703992v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:06:52,537] [INFO] Task started: fastANI
[2023-06-29 03:06:52,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b03ccde-13ea-4d31-8508-5f79f7c6b380/GCA_027039925.1_ASM2703992v1_genomic.fna.gz --refList GCA_027039925.1_ASM2703992v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027039925.1_ASM2703992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:07:04,205] [INFO] Task succeeded: fastANI
[2023-06-29 03:07:04,219] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 03:07:04,219] [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_015493675.1	s__M2005 sp015493675	99.3081	771	1116	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__M2005	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011192085.1	s__M2005 sp011192085	78.8038	247	1116	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__M2005	95.0	99.27	98.93	0.82	0.77	3	-
GCA_011371305.1	s__M2005 sp011371305	78.1697	215	1116	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__M2005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485435.1	s__M2005 sp015485435	77.2368	157	1116	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__M2005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011176555.1	s__DUEF01 sp011176555	76.7756	128	1116	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__DUEF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360575.1	s__JABWBG01 sp013360575	76.5515	155	1116	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__JABWBG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152585.1	s__JAADGC01 sp013152585	76.539	123	1116	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__JAADGC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694905.1	s__J102 sp003694905	76.142	78	1116	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__J102	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006569185.1	s__Litorilinea aerophila	75.9591	66	1116	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 03:07:04,221] [INFO] GTDB search result was written to GCA_027039925.1_ASM2703992v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:07:04,222] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:07:04,225] [INFO] DFAST_QC result json was written to GCA_027039925.1_ASM2703992v1_genomic.fna/dqc_result.json
[2023-06-29 03:07:04,225] [INFO] DFAST_QC completed!
[2023-06-29 03:07:04,225] [INFO] Total running time: 0h1m18s