[2023-06-19 00:58:11,120] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:58:11,305] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:58:11,305] [INFO] DQC Reference Directory: /var/lib/cwl/stga89bc41b-7656-485e-8bb9-e671ed67c806/dqc_reference
[2023-06-19 00:58:12,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:58:12,544] [INFO] Task started: Prodigal
[2023-06-19 00:58:12,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg365908bb-5298-4469-8713-16b75ed8e824/GCA_014859965.1_ASM1485996v1_genomic.fna.gz | prodigal -d GCA_014859965.1_ASM1485996v1_genomic.fna/cds.fna -a GCA_014859965.1_ASM1485996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:58:27,358] [INFO] Task succeeded: Prodigal
[2023-06-19 00:58:27,359] [INFO] Task started: HMMsearch
[2023-06-19 00:58:27,359] [INFO] Running command: hmmsearch --tblout GCA_014859965.1_ASM1485996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga89bc41b-7656-485e-8bb9-e671ed67c806/dqc_reference/reference_markers.hmm GCA_014859965.1_ASM1485996v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:58:27,604] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:58:27,607] [INFO] Found 6/6 markers.
[2023-06-19 00:58:27,648] [INFO] Query marker FASTA was written to GCA_014859965.1_ASM1485996v1_genomic.fna/markers.fasta
[2023-06-19 00:58:27,648] [INFO] Task started: Blastn
[2023-06-19 00:58:27,648] [INFO] Running command: blastn -query GCA_014859965.1_ASM1485996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga89bc41b-7656-485e-8bb9-e671ed67c806/dqc_reference/reference_markers.fasta -out GCA_014859965.1_ASM1485996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:58:28,227] [INFO] Task succeeded: Blastn
[2023-06-19 00:58:28,231] [INFO] Selected 22 target genomes.
[2023-06-19 00:58:28,231] [INFO] Target genome list was writen to GCA_014859965.1_ASM1485996v1_genomic.fna/target_genomes.txt
[2023-06-19 00:58:28,235] [INFO] Task started: fastANI
[2023-06-19 00:58:28,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg365908bb-5298-4469-8713-16b75ed8e824/GCA_014859965.1_ASM1485996v1_genomic.fna.gz --refList GCA_014859965.1_ASM1485996v1_genomic.fna/target_genomes.txt --output GCA_014859965.1_ASM1485996v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:58:42,859] [INFO] Task succeeded: fastANI
[2023-06-19 00:58:42,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga89bc41b-7656-485e-8bb9-e671ed67c806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:58:42,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga89bc41b-7656-485e-8bb9-e671ed67c806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:58:42,863] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:58:42,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 00:58:42,864] [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
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	75.3852	50	1665	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.332	53	1665	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:58:42,865] [INFO] DFAST Taxonomy check result was written to GCA_014859965.1_ASM1485996v1_genomic.fna/tc_result.tsv
[2023-06-19 00:58:42,866] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:58:42,866] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:58:42,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga89bc41b-7656-485e-8bb9-e671ed67c806/dqc_reference/checkm_data
[2023-06-19 00:58:42,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:58:42,916] [INFO] Task started: CheckM
[2023-06-19 00:58:42,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014859965.1_ASM1485996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014859965.1_ASM1485996v1_genomic.fna/checkm_input GCA_014859965.1_ASM1485996v1_genomic.fna/checkm_result
[2023-06-19 00:59:27,080] [INFO] Task succeeded: CheckM
[2023-06-19 00:59:27,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:59:27,103] [INFO] ===== Completeness check finished =====
[2023-06-19 00:59:27,104] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:59:27,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014859965.1_ASM1485996v1_genomic.fna/markers.fasta)
[2023-06-19 00:59:27,104] [INFO] Task started: Blastn
[2023-06-19 00:59:27,104] [INFO] Running command: blastn -query GCA_014859965.1_ASM1485996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga89bc41b-7656-485e-8bb9-e671ed67c806/dqc_reference/reference_markers_gtdb.fasta -out GCA_014859965.1_ASM1485996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:59:27,927] [INFO] Task succeeded: Blastn
[2023-06-19 00:59:27,932] [INFO] Selected 18 target genomes.
[2023-06-19 00:59:27,932] [INFO] Target genome list was writen to GCA_014859965.1_ASM1485996v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:59:27,939] [INFO] Task started: fastANI
[2023-06-19 00:59:27,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg365908bb-5298-4469-8713-16b75ed8e824/GCA_014859965.1_ASM1485996v1_genomic.fna.gz --refList GCA_014859965.1_ASM1485996v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014859965.1_ASM1485996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:59:41,852] [INFO] Task succeeded: fastANI
[2023-06-19 00:59:41,863] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:59:41,863] [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_014859965.1	s__JACZKQ01 sp014859965	100.0	1655	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__Anaerohalosphaeraceae;g__JACZKQ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003644175.1	s__B28-G16 sp003644175	76.7779	109	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__Anaerohalosphaeraceae;g__B28-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729675.1	s__T3Sed10-213 sp012729675	76.6318	81	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__Anaerohalosphaeraceae;g__T3Sed10-213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055475.1	s__DSDH01 sp011055475	76.5858	130	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__Anaerohalosphaeraceae;g__DSDH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018433925.1	s__JAHDQI01 sp018433925	76.5588	67	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__Anaerohalosphaeraceae;g__JAHDQI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011057845.1	s__UBA2266 sp011057845	76.4202	87	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__UBA2266	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048645.1	s__T3Sed10-213 sp011048645	76.3604	62	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__Anaerohalosphaeraceae;g__T3Sed10-213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016930745.1	s__JAFGGE01 sp016930745	76.3162	92	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__Anaerohalosphaeraceae;g__JAFGGE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517095.1	s__FEN-1350 sp012517095	76.0806	69	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__Anaerohalosphaeraceae;g__FEN-1350	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719085.1	s__PLanc-01 sp012719085	76.0609	110	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__PLanc-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517265.1	s__PLanc-01 sp012517265	75.7649	110	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__PLanc-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016928975.1	s__PLanc-01 sp016928975	75.5747	93	1665	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__SG8-4;g__PLanc-01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:59:41,866] [INFO] GTDB search result was written to GCA_014859965.1_ASM1485996v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:59:41,866] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:59:41,870] [INFO] DFAST_QC result json was written to GCA_014859965.1_ASM1485996v1_genomic.fna/dqc_result.json
[2023-06-19 00:59:41,870] [INFO] DFAST_QC completed!
[2023-06-19 00:59:41,870] [INFO] Total running time: 0h1m31s