[2023-06-29 18:37:31,832] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:37:31,839] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:37:31,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg231b517b-3434-47db-b2af-76d49f2d2d38/dqc_reference
[2023-06-29 18:37:33,085] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:37:33,085] [INFO] Task started: Prodigal
[2023-06-29 18:37:33,086] [INFO] Running command: gunzip -c /var/lib/cwl/stgd647b8d7-b941-4571-ae85-992324d4efcb/GCA_011050585.1_ASM1105058v1_genomic.fna.gz | prodigal -d GCA_011050585.1_ASM1105058v1_genomic.fna/cds.fna -a GCA_011050585.1_ASM1105058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:37:47,909] [INFO] Task succeeded: Prodigal
[2023-06-29 18:37:47,910] [INFO] Task started: HMMsearch
[2023-06-29 18:37:47,910] [INFO] Running command: hmmsearch --tblout GCA_011050585.1_ASM1105058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg231b517b-3434-47db-b2af-76d49f2d2d38/dqc_reference/reference_markers.hmm GCA_011050585.1_ASM1105058v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:37:48,199] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:37:48,200] [INFO] Found 6/6 markers.
[2023-06-29 18:37:48,237] [INFO] Query marker FASTA was written to GCA_011050585.1_ASM1105058v1_genomic.fna/markers.fasta
[2023-06-29 18:37:48,238] [INFO] Task started: Blastn
[2023-06-29 18:37:48,238] [INFO] Running command: blastn -query GCA_011050585.1_ASM1105058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg231b517b-3434-47db-b2af-76d49f2d2d38/dqc_reference/reference_markers.fasta -out GCA_011050585.1_ASM1105058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:37:49,038] [INFO] Task succeeded: Blastn
[2023-06-29 18:37:49,044] [INFO] Selected 19 target genomes.
[2023-06-29 18:37:49,044] [INFO] Target genome list was writen to GCA_011050585.1_ASM1105058v1_genomic.fna/target_genomes.txt
[2023-06-29 18:37:49,047] [INFO] Task started: fastANI
[2023-06-29 18:37:49,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgd647b8d7-b941-4571-ae85-992324d4efcb/GCA_011050585.1_ASM1105058v1_genomic.fna.gz --refList GCA_011050585.1_ASM1105058v1_genomic.fna/target_genomes.txt --output GCA_011050585.1_ASM1105058v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:38:03,955] [INFO] Task succeeded: fastANI
[2023-06-29 18:38:03,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg231b517b-3434-47db-b2af-76d49f2d2d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:38:03,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg231b517b-3434-47db-b2af-76d49f2d2d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:38:03,969] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 18:38:03,969] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 18:38:03,970] [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
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	98.5462	1015	1343	95	conclusive
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	88.1549	942	1343	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	79.6399	556	1343	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	79.4575	449	1343	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	79.3692	436	1343	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.6937	481	1343	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.6784	477	1343	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	78.3512	427	1343	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.9625	397	1343	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.8542	411	1343	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.8241	359	1343	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.8854	244	1343	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	76.6746	246	1343	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.5849	128	1343	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.4424	227	1343	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.3942	125	1343	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 18:38:03,973] [INFO] DFAST Taxonomy check result was written to GCA_011050585.1_ASM1105058v1_genomic.fna/tc_result.tsv
[2023-06-29 18:38:03,974] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:38:03,974] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:38:03,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg231b517b-3434-47db-b2af-76d49f2d2d38/dqc_reference/checkm_data
[2023-06-29 18:38:03,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:38:04,020] [INFO] Task started: CheckM
[2023-06-29 18:38:04,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011050585.1_ASM1105058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011050585.1_ASM1105058v1_genomic.fna/checkm_input GCA_011050585.1_ASM1105058v1_genomic.fna/checkm_result
[2023-06-29 18:38:47,943] [INFO] Task succeeded: CheckM
[2023-06-29 18:38:47,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 18:38:47,968] [INFO] ===== Completeness check finished =====
[2023-06-29 18:38:47,969] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:38:47,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011050585.1_ASM1105058v1_genomic.fna/markers.fasta)
[2023-06-29 18:38:47,969] [INFO] Task started: Blastn
[2023-06-29 18:38:47,970] [INFO] Running command: blastn -query GCA_011050585.1_ASM1105058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg231b517b-3434-47db-b2af-76d49f2d2d38/dqc_reference/reference_markers_gtdb.fasta -out GCA_011050585.1_ASM1105058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:38:49,294] [INFO] Task succeeded: Blastn
[2023-06-29 18:38:49,299] [INFO] Selected 10 target genomes.
[2023-06-29 18:38:49,299] [INFO] Target genome list was writen to GCA_011050585.1_ASM1105058v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:38:49,305] [INFO] Task started: fastANI
[2023-06-29 18:38:49,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgd647b8d7-b941-4571-ae85-992324d4efcb/GCA_011050585.1_ASM1105058v1_genomic.fna.gz --refList GCA_011050585.1_ASM1105058v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011050585.1_ASM1105058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:38:57,284] [INFO] Task succeeded: fastANI
[2023-06-29 18:38:57,298] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 18:38:57,299] [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_900103185.1	s__Sulfitobacter litoralis	98.4973	1018	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	conclusive
GCF_006064855.1	s__Sulfitobacter sp006064855	94.7758	915	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	88.1549	942	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_013282155.1	s__Sulfitobacter sp013282155	80.7843	647	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	80.3595	627	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	80.0651	498	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	79.644	555	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.7247	466	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.464	342	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	76.6738	246	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 18:38:57,301] [INFO] GTDB search result was written to GCA_011050585.1_ASM1105058v1_genomic.fna/result_gtdb.tsv
[2023-06-29 18:38:57,301] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:38:57,305] [INFO] DFAST_QC result json was written to GCA_011050585.1_ASM1105058v1_genomic.fna/dqc_result.json
[2023-06-29 18:38:57,305] [INFO] DFAST_QC completed!
[2023-06-29 18:38:57,305] [INFO] Total running time: 0h1m25s