[2023-06-07 21:53:18,687] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:53:18,697] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:53:18,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg537ef38a-a9fd-4783-8f3f-c17e17a9008c/dqc_reference
[2023-06-07 21:53:21,661] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:53:21,662] [INFO] Task started: Prodigal
[2023-06-07 21:53:21,663] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9e7a350-5900-49b5-bdc5-3cc6c8c232e4/GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna.gz | prodigal -d GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/cds.fna -a GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:53:25,567] [INFO] Task succeeded: Prodigal
[2023-06-07 21:53:25,567] [INFO] Task started: HMMsearch
[2023-06-07 21:53:25,568] [INFO] Running command: hmmsearch --tblout GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg537ef38a-a9fd-4783-8f3f-c17e17a9008c/dqc_reference/reference_markers.hmm GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:53:25,813] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:53:25,814] [INFO] Found 6/6 markers.
[2023-06-07 21:53:25,834] [INFO] Query marker FASTA was written to GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/markers.fasta
[2023-06-07 21:53:25,834] [INFO] Task started: Blastn
[2023-06-07 21:53:25,834] [INFO] Running command: blastn -query GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/markers.fasta -db /var/lib/cwl/stg537ef38a-a9fd-4783-8f3f-c17e17a9008c/dqc_reference/reference_markers.fasta -out GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:53:26,460] [INFO] Task succeeded: Blastn
[2023-06-07 21:53:26,464] [INFO] Selected 32 target genomes.
[2023-06-07 21:53:26,465] [INFO] Target genome list was writen to GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/target_genomes.txt
[2023-06-07 21:53:26,469] [INFO] Task started: fastANI
[2023-06-07 21:53:26,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9e7a350-5900-49b5-bdc5-3cc6c8c232e4/GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna.gz --refList GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/target_genomes.txt --output GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:53:42,251] [INFO] Task succeeded: fastANI
[2023-06-07 21:53:42,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg537ef38a-a9fd-4783-8f3f-c17e17a9008c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:53:42,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg537ef38a-a9fd-4783-8f3f-c17e17a9008c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:53:42,259] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:53:42,259] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:53:42,260] [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
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	77.3234	66	657	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	77.2731	67	657	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	77.2479	55	657	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	77.0932	57	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:53:42,261] [INFO] DFAST Taxonomy check result was written to GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/tc_result.tsv
[2023-06-07 21:53:42,262] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:53:42,262] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:53:42,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg537ef38a-a9fd-4783-8f3f-c17e17a9008c/dqc_reference/checkm_data
[2023-06-07 21:53:42,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:53:42,291] [INFO] Task started: CheckM
[2023-06-07 21:53:42,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/checkm_input GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/checkm_result
[2023-06-07 21:54:01,751] [INFO] Task succeeded: CheckM
[2023-06-07 21:54:01,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:54:01,776] [INFO] ===== Completeness check finished =====
[2023-06-07 21:54:01,777] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:54:01,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/markers.fasta)
[2023-06-07 21:54:01,777] [INFO] Task started: Blastn
[2023-06-07 21:54:01,778] [INFO] Running command: blastn -query GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/markers.fasta -db /var/lib/cwl/stg537ef38a-a9fd-4783-8f3f-c17e17a9008c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:54:02,809] [INFO] Task succeeded: Blastn
[2023-06-07 21:54:02,814] [INFO] Selected 23 target genomes.
[2023-06-07 21:54:02,815] [INFO] Target genome list was writen to GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:54:02,820] [INFO] Task started: fastANI
[2023-06-07 21:54:02,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9e7a350-5900-49b5-bdc5-3cc6c8c232e4/GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna.gz --refList GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/target_genomes_gtdb.txt --output GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:54:13,255] [INFO] Task succeeded: fastANI
[2023-06-07 21:54:13,267] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:54:13,267] [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_900315425.1	s__CAG-603 sp900315425	100.0	653	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.93	98.30	0.88	0.81	6	conclusive
GCA_900110975.1	s__CAG-603 sp900110975	78.4583	178	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.39	98.39	0.96	0.96	2	-
GCA_900314525.1	s__CAG-603 sp900314525	78.2334	105	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.63	99.55	0.90	0.85	5	-
GCA_017412055.1	s__CAG-303 sp017412055	78.0782	54	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362455.1	s__CAG-603 sp900066105	78.0182	115	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.95	98.18	0.94	0.88	5	-
GCA_900314555.1	s__CAG-603 sp900314555	77.8171	118	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002351535.1	s__UBA2821 sp002351535	77.5093	83	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	99.98	99.98	0.97	0.97	2	-
GCA_017416465.1	s__CAG-603 sp017416465	77.4822	90	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363805.1	s__Eubacterium_G sp000434315	77.4685	63	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
GCA_900548465.1	s__Eubacterium_G sp900548465	77.1905	56	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	97.75	97.64	0.80	0.72	3	-
GCA_014799465.1	s__UBA2821 sp014799465	77.1533	63	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321855.1	s__CAG-603 sp900321855	76.5577	78	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.42	99.42	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-07 21:54:13,269] [INFO] GTDB search result was written to GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/result_gtdb.tsv
[2023-06-07 21:54:13,270] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:54:13,273] [INFO] DFAST_QC result json was written to GCA_902755005.1_Rumen_uncultured_genome_RUG10016_genomic.fna/dqc_result.json
[2023-06-07 21:54:13,273] [INFO] DFAST_QC completed!
[2023-06-07 21:54:13,273] [INFO] Total running time: 0h0m55s