[2023-06-05 10:46:57,377] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:46:57,381] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:46:57,381] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0f877b2-573d-4094-adb4-147a180aa36b/dqc_reference
[2023-06-05 10:46:59,024] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:46:59,026] [INFO] Task started: Prodigal
[2023-06-05 10:46:59,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg93007cc8-19be-44f6-a581-7ae3fb6e52ed/GCA_904386275.1_Chicken_23_mag_100_genomic.fna.gz | prodigal -d GCA_904386275.1_Chicken_23_mag_100_genomic.fna/cds.fna -a GCA_904386275.1_Chicken_23_mag_100_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:47:04,736] [INFO] Task succeeded: Prodigal
[2023-06-05 10:47:04,737] [INFO] Task started: HMMsearch
[2023-06-05 10:47:04,737] [INFO] Running command: hmmsearch --tblout GCA_904386275.1_Chicken_23_mag_100_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0f877b2-573d-4094-adb4-147a180aa36b/dqc_reference/reference_markers.hmm GCA_904386275.1_Chicken_23_mag_100_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:47:04,938] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:47:04,939] [INFO] Found 6/6 markers.
[2023-06-05 10:47:04,960] [INFO] Query marker FASTA was written to GCA_904386275.1_Chicken_23_mag_100_genomic.fna/markers.fasta
[2023-06-05 10:47:04,960] [INFO] Task started: Blastn
[2023-06-05 10:47:04,960] [INFO] Running command: blastn -query GCA_904386275.1_Chicken_23_mag_100_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0f877b2-573d-4094-adb4-147a180aa36b/dqc_reference/reference_markers.fasta -out GCA_904386275.1_Chicken_23_mag_100_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:05,712] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:05,715] [INFO] Selected 23 target genomes.
[2023-06-05 10:47:05,715] [INFO] Target genome list was writen to GCA_904386275.1_Chicken_23_mag_100_genomic.fna/target_genomes.txt
[2023-06-05 10:47:05,720] [INFO] Task started: fastANI
[2023-06-05 10:47:05,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg93007cc8-19be-44f6-a581-7ae3fb6e52ed/GCA_904386275.1_Chicken_23_mag_100_genomic.fna.gz --refList GCA_904386275.1_Chicken_23_mag_100_genomic.fna/target_genomes.txt --output GCA_904386275.1_Chicken_23_mag_100_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:47:17,728] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:17,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0f877b2-573d-4094-adb4-147a180aa36b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:47:17,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0f877b2-573d-4094-adb4-147a180aa36b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:47:17,737] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:47:17,737] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:47:17,737] [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
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	77.256	96	769	95	below_threshold
Hydrogeniiclostridium mannosilyticum	strain=ASD2818	GCA_003268275.1	2764322	2764322	type	True	77.0945	67	769	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.0543	127	769	95	below_threshold
Caproicibacter fermentans	strain=EA1	GCA_009746625.1	2576756	2576756	type	True	76.6441	56	769	95	below_threshold
Feifania hominis	strain=BX7	GCA_014384765.1	2763660	2763660	type	True	76.614	73	769	95	below_threshold
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	76.5968	82	769	95	below_threshold
Neglectibacter timonensis	strain=SN17	GCA_900048895.1	1776382	1776382	type	True	76.5399	75	769	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	76.3889	53	769	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.3013	67	769	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.217	55	769	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	76.1979	59	769	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	75.0058	51	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:47:17,739] [INFO] DFAST Taxonomy check result was written to GCA_904386275.1_Chicken_23_mag_100_genomic.fna/tc_result.tsv
[2023-06-05 10:47:17,740] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:47:17,740] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:47:17,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0f877b2-573d-4094-adb4-147a180aa36b/dqc_reference/checkm_data
[2023-06-05 10:47:17,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:47:17,766] [INFO] Task started: CheckM
[2023-06-05 10:47:17,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_904386275.1_Chicken_23_mag_100_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_904386275.1_Chicken_23_mag_100_genomic.fna/checkm_input GCA_904386275.1_Chicken_23_mag_100_genomic.fna/checkm_result
[2023-06-05 10:47:38,525] [INFO] Task succeeded: CheckM
[2023-06-05 10:47:38,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:47:38,542] [INFO] ===== Completeness check finished =====
[2023-06-05 10:47:38,542] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:47:38,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_904386275.1_Chicken_23_mag_100_genomic.fna/markers.fasta)
[2023-06-05 10:47:38,544] [INFO] Task started: Blastn
[2023-06-05 10:47:38,544] [INFO] Running command: blastn -query GCA_904386275.1_Chicken_23_mag_100_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0f877b2-573d-4094-adb4-147a180aa36b/dqc_reference/reference_markers_gtdb.fasta -out GCA_904386275.1_Chicken_23_mag_100_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:39,974] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:39,977] [INFO] Selected 9 target genomes.
[2023-06-05 10:47:39,977] [INFO] Target genome list was writen to GCA_904386275.1_Chicken_23_mag_100_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:47:39,984] [INFO] Task started: fastANI
[2023-06-05 10:47:39,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg93007cc8-19be-44f6-a581-7ae3fb6e52ed/GCA_904386275.1_Chicken_23_mag_100_genomic.fna.gz --refList GCA_904386275.1_Chicken_23_mag_100_genomic.fna/target_genomes_gtdb.txt --output GCA_904386275.1_Chicken_23_mag_100_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:47:44,143] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:44,150] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:47:44,150] [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_900552925.1	s__UBA1417 sp900552925	97.8765	399	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.06	97.73	0.91	0.83	5	conclusive
GCA_900549945.1	s__UBA1417 sp900549945	88.2032	426	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.46	97.65	0.85	0.74	4	-
GCA_002305575.1	s__UBA1417 sp002305575	83.1901	527	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.68	98.68	0.86	0.86	2	-
GCA_004555625.1	s__UBA1417 sp004555625	83.1767	479	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008681155.1	s__UBA1417 sp003531055	79.9488	386	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	97.97	97.38	0.92	0.84	13	-
GCA_017407665.1	s__UBA1417 sp017407665	79.5559	281	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017623855.1	s__UBA1417 sp017623855	79.3044	213	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015667585.1	s__Anaeromassilibacillus sp015667585	77.136	112	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317025.1	s__RUG592 sp900317025	76.4878	53	769	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG592	95.0	99.45	99.45	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-05 10:47:44,152] [INFO] GTDB search result was written to GCA_904386275.1_Chicken_23_mag_100_genomic.fna/result_gtdb.tsv
[2023-06-05 10:47:44,152] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:47:44,155] [INFO] DFAST_QC result json was written to GCA_904386275.1_Chicken_23_mag_100_genomic.fna/dqc_result.json
[2023-06-05 10:47:44,155] [INFO] DFAST_QC completed!
[2023-06-05 10:47:44,155] [INFO] Total running time: 0h0m47s