[2023-06-29 12:49:36,260] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:49:36,280] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:49:36,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg586d6b5c-268b-4c41-81b8-9641a828616e/dqc_reference
[2023-06-29 12:49:37,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:49:37,468] [INFO] Task started: Prodigal
[2023-06-29 12:49:37,468] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6eb422c-1dac-4e8d-b099-b1f6224f1f07/GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:49:44,140] [INFO] Task succeeded: Prodigal
[2023-06-29 12:49:44,140] [INFO] Task started: HMMsearch
[2023-06-29 12:49:44,140] [INFO] Running command: hmmsearch --tblout GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg586d6b5c-268b-4c41-81b8-9641a828616e/dqc_reference/reference_markers.hmm GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:49:44,448] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:49:44,450] [INFO] Found 6/6 markers.
[2023-06-29 12:49:44,484] [INFO] Query marker FASTA was written to GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 12:49:44,485] [INFO] Task started: Blastn
[2023-06-29 12:49:44,485] [INFO] Running command: blastn -query GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg586d6b5c-268b-4c41-81b8-9641a828616e/dqc_reference/reference_markers.fasta -out GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:49:45,197] [INFO] Task succeeded: Blastn
[2023-06-29 12:49:45,200] [INFO] Selected 12 target genomes.
[2023-06-29 12:49:45,201] [INFO] Target genome list was writen to GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 12:49:45,204] [INFO] Task started: fastANI
[2023-06-29 12:49:45,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6eb422c-1dac-4e8d-b099-b1f6224f1f07/GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:49:52,758] [INFO] Task succeeded: fastANI
[2023-06-29 12:49:52,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg586d6b5c-268b-4c41-81b8-9641a828616e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:49:52,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg586d6b5c-268b-4c41-81b8-9641a828616e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:49:52,769] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:49:52,769] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:49:52,769] [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
Desulfomicrobium escambiense	strain=DSM 10707	GCA_000428825.1	29503	29503	type	True	80.7379	423	636	95	below_threshold
Desulfomicrobium baculatum	strain=DSM 4028	GCA_000023225.1	899	899	type	True	79.5441	358	636	95	below_threshold
Desulfomicrobium apsheronum	strain=DSM 5918	GCA_900114115.1	52560	52560	type	True	79.3357	370	636	95	below_threshold
Desulfomicrobium orale	strain=DSM 12838	GCA_001553625.1	132132	132132	type	True	77.9668	209	636	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	76.5681	73	636	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	76.4994	89	636	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	76.3092	100	636	95	below_threshold
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	76.2586	83	636	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	76.2432	72	636	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	76.2214	71	636	95	below_threshold
Desulfonatronum lacustre	strain=DSM 10312	GCA_000519265.1	66849	66849	type	True	76.104	68	636	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:49:52,771] [INFO] DFAST Taxonomy check result was written to GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 12:49:52,772] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:49:52,772] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:49:52,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg586d6b5c-268b-4c41-81b8-9641a828616e/dqc_reference/checkm_data
[2023-06-29 12:49:52,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:49:52,804] [INFO] Task started: CheckM
[2023-06-29 12:49:52,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 12:50:19,210] [INFO] Task succeeded: CheckM
[2023-06-29 12:50:19,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:50:19,232] [INFO] ===== Completeness check finished =====
[2023-06-29 12:50:19,232] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:50:19,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 12:50:19,233] [INFO] Task started: Blastn
[2023-06-29 12:50:19,233] [INFO] Running command: blastn -query GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg586d6b5c-268b-4c41-81b8-9641a828616e/dqc_reference/reference_markers_gtdb.fasta -out GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:50:20,023] [INFO] Task succeeded: Blastn
[2023-06-29 12:50:20,027] [INFO] Selected 12 target genomes.
[2023-06-29 12:50:20,027] [INFO] Target genome list was writen to GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:50:20,041] [INFO] Task started: fastANI
[2023-06-29 12:50:20,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6eb422c-1dac-4e8d-b099-b1f6224f1f07/GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:50:27,182] [INFO] Task succeeded: fastANI
[2023-06-29 12:50:27,195] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:50:27,195] [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_012729655.1	s__Desulfomicrobium sp012729655	99.2788	553	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000428825.1	s__Desulfomicrobium escambiense	80.7287	424	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003542385.1	s__Desulfomicrobium sp003542385	80.2492	283	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023225.1	s__Desulfomicrobium baculatum	79.5512	357	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873765.1	s__Desulfomicrobium macestii	79.5155	370	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	98.27	98.27	0.85	0.85	2	-
GCA_018902545.1	s__Desulfomicrobium sp018902545	79.4672	355	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	99.99	99.98	0.99	0.97	6	-
GCA_002412965.1	s__Desulfomicrobium sp002412965	79.3197	392	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114115.1	s__Desulfomicrobium apsheronum	79.304	373	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009930495.1	s__Desulfomicrobium sp009930495	78.6582	268	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553625.1	s__Desulfomicrobium orale	77.9499	210	636	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:50:27,198] [INFO] GTDB search result was written to GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 12:50:27,198] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:50:27,202] [INFO] DFAST_QC result json was written to GCA_937862785.1_SRR8868559_bin.55_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 12:50:27,202] [INFO] DFAST_QC completed!
[2023-06-29 12:50:27,202] [INFO] Total running time: 0h0m51s