[2024-01-24 12:46:34,815] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:34,817] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:34,817] [INFO] DQC Reference Directory: /var/lib/cwl/stg35330068-bbc5-4672-914a-9781483a5c3f/dqc_reference
[2024-01-24 12:46:35,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:35,942] [INFO] Task started: Prodigal
[2024-01-24 12:46:35,942] [INFO] Running command: gunzip -c /var/lib/cwl/stg74e7167d-3413-481a-b855-bde78f544f94/GCF_003312875.1_ASM331287v1_genomic.fna.gz | prodigal -d GCF_003312875.1_ASM331287v1_genomic.fna/cds.fna -a GCF_003312875.1_ASM331287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:08,233] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:08,233] [INFO] Task started: HMMsearch
[2024-01-24 12:47:08,233] [INFO] Running command: hmmsearch --tblout GCF_003312875.1_ASM331287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35330068-bbc5-4672-914a-9781483a5c3f/dqc_reference/reference_markers.hmm GCF_003312875.1_ASM331287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:08,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:08,595] [INFO] Found 6/6 markers.
[2024-01-24 12:47:08,663] [INFO] Query marker FASTA was written to GCF_003312875.1_ASM331287v1_genomic.fna/markers.fasta
[2024-01-24 12:47:08,663] [INFO] Task started: Blastn
[2024-01-24 12:47:08,663] [INFO] Running command: blastn -query GCF_003312875.1_ASM331287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35330068-bbc5-4672-914a-9781483a5c3f/dqc_reference/reference_markers.fasta -out GCF_003312875.1_ASM331287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:10,001] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:10,005] [INFO] Selected 20 target genomes.
[2024-01-24 12:47:10,005] [INFO] Target genome list was writen to GCF_003312875.1_ASM331287v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:10,011] [INFO] Task started: fastANI
[2024-01-24 12:47:10,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e7167d-3413-481a-b855-bde78f544f94/GCF_003312875.1_ASM331287v1_genomic.fna.gz --refList GCF_003312875.1_ASM331287v1_genomic.fna/target_genomes.txt --output GCF_003312875.1_ASM331287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:55,077] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:55,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35330068-bbc5-4672-914a-9781483a5c3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:55,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35330068-bbc5-4672-914a-9781483a5c3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:55,092] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:55,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:55,093] [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
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	100.0	3040	3040	95	conclusive
Amycolatopsis magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	88.9336	2319	3040	95	below_threshold
Amycolatopsis suaedae	strain=8-3EHSu	GCA_004214935.1	2510978	2510978	type	True	81.4191	1517	3040	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	81.1967	1522	3040	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	80.7449	1517	3040	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.5829	1289	3040	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	80.5147	1261	3040	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	80.5128	1250	3040	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	80.3363	1422	3040	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	80.2985	1558	3040	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	80.2934	1155	3040	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	80.2272	1259	3040	95	below_threshold
Amycolatopsis sulphurea	strain=DSM 46092	GCA_002564045.1	76022	76022	type	True	80.1985	1047	3040	95	below_threshold
Amycolatopsis pretoriensis	strain=DSM 44654	GCA_900107925.1	218821	218821	type	True	80.1936	1466	3040	95	below_threshold
Amycolatopsis pittospori	strain=PIP199	GCA_013870525.1	2749434	2749434	type	True	80.1925	1318	3040	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	80.1783	1481	3040	95	below_threshold
Amycolatopsis japonica	strain=MG417-CF17	GCA_000732925.1	208439	208439	type	True	80.1231	1422	3040	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	79.9443	1514	3040	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.8038	1178	3040	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.625	949	3040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:55,094] [INFO] DFAST Taxonomy check result was written to GCF_003312875.1_ASM331287v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:55,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:55,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:55,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35330068-bbc5-4672-914a-9781483a5c3f/dqc_reference/checkm_data
[2024-01-24 12:47:55,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:55,175] [INFO] Task started: CheckM
[2024-01-24 12:47:55,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003312875.1_ASM331287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003312875.1_ASM331287v1_genomic.fna/checkm_input GCF_003312875.1_ASM331287v1_genomic.fna/checkm_result
[2024-01-24 12:50:33,739] [INFO] Task succeeded: CheckM
[2024-01-24 12:50:33,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:50:33,765] [INFO] ===== Completeness check finished =====
[2024-01-24 12:50:33,766] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:50:33,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003312875.1_ASM331287v1_genomic.fna/markers.fasta)
[2024-01-24 12:50:33,766] [INFO] Task started: Blastn
[2024-01-24 12:50:33,766] [INFO] Running command: blastn -query GCF_003312875.1_ASM331287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35330068-bbc5-4672-914a-9781483a5c3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003312875.1_ASM331287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:50:35,756] [INFO] Task succeeded: Blastn
[2024-01-24 12:50:35,759] [INFO] Selected 9 target genomes.
[2024-01-24 12:50:35,760] [INFO] Target genome list was writen to GCF_003312875.1_ASM331287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:50:35,781] [INFO] Task started: fastANI
[2024-01-24 12:50:35,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e7167d-3413-481a-b855-bde78f544f94/GCF_003312875.1_ASM331287v1_genomic.fna.gz --refList GCF_003312875.1_ASM331287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003312875.1_ASM331287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:51:00,307] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:00,316] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:51:00,316] [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
GCF_003312875.1	s__Amycolatopsis albispora	100.0	3039	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009429145.1	s__Amycolatopsis sp009429145	90.7631	2502	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309385.1	s__Amycolatopsis sp017309385	90.5547	2481	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875555.1	s__Amycolatopsis magusensis	88.9352	2319	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214935.1	s__Amycolatopsis suaedae	81.3998	1521	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384315.1	s__Amycolatopsis nigrescens	81.1545	1534	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	80.7746	1512	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736145.1	s__Amycolatopsis sp018736145	80.3489	1476	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105945.1	s__Amycolatopsis tolypomycina	80.1719	1483	3040	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:51:00,320] [INFO] GTDB search result was written to GCF_003312875.1_ASM331287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:51:00,320] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:51:00,324] [INFO] DFAST_QC result json was written to GCF_003312875.1_ASM331287v1_genomic.fna/dqc_result.json
[2024-01-24 12:51:00,324] [INFO] DFAST_QC completed!
[2024-01-24 12:51:00,324] [INFO] Total running time: 0h4m26s