[2023-06-27 11:48:42,978] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:48:42,980] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:48:42,980] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb1ef08d-a837-4bf8-ab3e-19377ca7028f/dqc_reference
[2023-06-27 11:48:44,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:48:44,358] [INFO] Task started: Prodigal
[2023-06-27 11:48:44,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a190bd9-e59f-445c-a21f-606ec58d0edf/GCA_027483175.1_ASM2748317v1_genomic.fna.gz | prodigal -d GCA_027483175.1_ASM2748317v1_genomic.fna/cds.fna -a GCA_027483175.1_ASM2748317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:49:22,148] [INFO] Task succeeded: Prodigal
[2023-06-27 11:49:22,150] [INFO] Task started: HMMsearch
[2023-06-27 11:49:22,150] [INFO] Running command: hmmsearch --tblout GCA_027483175.1_ASM2748317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb1ef08d-a837-4bf8-ab3e-19377ca7028f/dqc_reference/reference_markers.hmm GCA_027483175.1_ASM2748317v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:49:22,465] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:49:22,467] [INFO] Found 6/6 markers.
[2023-06-27 11:49:22,528] [INFO] Query marker FASTA was written to GCA_027483175.1_ASM2748317v1_genomic.fna/markers.fasta
[2023-06-27 11:49:22,528] [INFO] Task started: Blastn
[2023-06-27 11:49:22,528] [INFO] Running command: blastn -query GCA_027483175.1_ASM2748317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1ef08d-a837-4bf8-ab3e-19377ca7028f/dqc_reference/reference_markers.fasta -out GCA_027483175.1_ASM2748317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:49:23,111] [INFO] Task succeeded: Blastn
[2023-06-27 11:49:23,116] [INFO] Selected 30 target genomes.
[2023-06-27 11:49:23,117] [INFO] Target genome list was writen to GCA_027483175.1_ASM2748317v1_genomic.fna/target_genomes.txt
[2023-06-27 11:49:23,126] [INFO] Task started: fastANI
[2023-06-27 11:49:23,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a190bd9-e59f-445c-a21f-606ec58d0edf/GCA_027483175.1_ASM2748317v1_genomic.fna.gz --refList GCA_027483175.1_ASM2748317v1_genomic.fna/target_genomes.txt --output GCA_027483175.1_ASM2748317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:49:54,078] [INFO] Task succeeded: fastANI
[2023-06-27 11:49:54,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb1ef08d-a837-4bf8-ab3e-19377ca7028f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:49:54,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb1ef08d-a837-4bf8-ab3e-19377ca7028f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:49:54,092] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:49:54,093] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:49:54,093] [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
Akkermansia glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	75.7895	52	1768	95	below_threshold
Prosthecobacter fusiformis	strain=ATCC 25309	GCA_004364345.1	48464	48464	type	True	75.7368	60	1768	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	75.5731	78	1768	95	below_threshold
Verrucomicrobium spinosum	strain=JCM 18804	GCA_001313125.1	2736	2736	type	True	75.5713	76	1768	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	75.3524	75	1768	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	74.7334	53	1768	95	below_threshold
Corallococcus aberystwythensis	strain=AB050A	GCA_003612165.1	2316722	2316722	type	True	74.6965	75	1768	95	below_threshold
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	74.6645	79	1768	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	74.6068	73	1768	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.5469	81	1768	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	74.5452	80	1768	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:49:54,109] [INFO] DFAST Taxonomy check result was written to GCA_027483175.1_ASM2748317v1_genomic.fna/tc_result.tsv
[2023-06-27 11:49:54,110] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:49:54,110] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:49:54,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb1ef08d-a837-4bf8-ab3e-19377ca7028f/dqc_reference/checkm_data
[2023-06-27 11:49:54,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:49:54,182] [INFO] Task started: CheckM
[2023-06-27 11:49:54,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027483175.1_ASM2748317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027483175.1_ASM2748317v1_genomic.fna/checkm_input GCA_027483175.1_ASM2748317v1_genomic.fna/checkm_result
[2023-06-27 11:51:40,139] [INFO] Task succeeded: CheckM
[2023-06-27 11:51:40,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:51:40,172] [INFO] ===== Completeness check finished =====
[2023-06-27 11:51:40,173] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:51:40,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027483175.1_ASM2748317v1_genomic.fna/markers.fasta)
[2023-06-27 11:51:40,174] [INFO] Task started: Blastn
[2023-06-27 11:51:40,175] [INFO] Running command: blastn -query GCA_027483175.1_ASM2748317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1ef08d-a837-4bf8-ab3e-19377ca7028f/dqc_reference/reference_markers_gtdb.fasta -out GCA_027483175.1_ASM2748317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:51:41,098] [INFO] Task succeeded: Blastn
[2023-06-27 11:51:41,107] [INFO] Selected 30 target genomes.
[2023-06-27 11:51:41,107] [INFO] Target genome list was writen to GCA_027483175.1_ASM2748317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:51:41,124] [INFO] Task started: fastANI
[2023-06-27 11:51:41,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a190bd9-e59f-445c-a21f-606ec58d0edf/GCA_027483175.1_ASM2748317v1_genomic.fna.gz --refList GCA_027483175.1_ASM2748317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027483175.1_ASM2748317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:52:08,070] [INFO] Task succeeded: fastANI
[2023-06-27 11:52:08,087] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:52:08,087] [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_003402705.1	s__V1-33 sp003402705	93.2613	1050	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__V1-33;g__V1-33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005787565.1	s__Luteolibacter sp005787565	76.2038	140	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838675.1	s__Prosthecobacter sp903838675	76.0894	108	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.92	99.91	0.96	0.96	3	-
GCA_004293445.1	s__Haloferula sp004293445	75.9532	60	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	99.99	99.98	0.97	0.96	4	-
GCA_018003315.1	s__JAGNEJ01 sp018003315	75.9445	91	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__V1-33;g__JAGNEJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	75.7484	56	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017798145.1	s__Luteolibacter sp017798145	75.7409	74	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879935.1	s__Prosthecobacter sp014879935	75.6631	119	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739635.1	s__Verrucomicrobium sp000739635	75.6287	70	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904755.1	s__Haloferula sp014904755	75.5972	93	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	75.4211	81	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970725.1	s__V1-115 sp018970725	75.3497	54	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__V1-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123195.1	s__SKLO01 sp007123195	75.1579	85	1768	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__SKLO01;g__SKLO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612165.1	s__Corallococcus aberystwythensis	74.6953	74	1768	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611695.1	s__Corallococcus carmarthensis	74.6118	70	1768	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173515.1	s__Corallococcus sp004173515	74.5817	59	1768	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111765.1	s__Myxococcus fulvus	74.5468	81	1768	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.03	95.70	0.96	0.91	4	-
--------------------------------------------------------------------------------
[2023-06-27 11:52:08,121] [INFO] GTDB search result was written to GCA_027483175.1_ASM2748317v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:52:08,123] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:52:08,129] [INFO] DFAST_QC result json was written to GCA_027483175.1_ASM2748317v1_genomic.fna/dqc_result.json
[2023-06-27 11:52:08,129] [INFO] DFAST_QC completed!
[2023-06-27 11:52:08,129] [INFO] Total running time: 0h3m25s