[2023-06-08 03:42:22,372] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:42:22,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:42:22,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg74fe3476-c3a2-4aa1-a081-d06778663a57/dqc_reference
[2023-06-08 03:42:23,678] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:42:23,679] [INFO] Task started: Prodigal
[2023-06-08 03:42:23,680] [INFO] Running command: gunzip -c /var/lib/cwl/stg1746376b-c1d0-45ca-92b2-333d38f87354/GCA_945862235.1_MH-08apr19-81_genomic.fna.gz | prodigal -d GCA_945862235.1_MH-08apr19-81_genomic.fna/cds.fna -a GCA_945862235.1_MH-08apr19-81_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:42:43,339] [INFO] Task succeeded: Prodigal
[2023-06-08 03:42:43,340] [INFO] Task started: HMMsearch
[2023-06-08 03:42:43,340] [INFO] Running command: hmmsearch --tblout GCA_945862235.1_MH-08apr19-81_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74fe3476-c3a2-4aa1-a081-d06778663a57/dqc_reference/reference_markers.hmm GCA_945862235.1_MH-08apr19-81_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:42:43,686] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:42:43,688] [INFO] Found 6/6 markers.
[2023-06-08 03:42:43,742] [INFO] Query marker FASTA was written to GCA_945862235.1_MH-08apr19-81_genomic.fna/markers.fasta
[2023-06-08 03:42:43,742] [INFO] Task started: Blastn
[2023-06-08 03:42:43,742] [INFO] Running command: blastn -query GCA_945862235.1_MH-08apr19-81_genomic.fna/markers.fasta -db /var/lib/cwl/stg74fe3476-c3a2-4aa1-a081-d06778663a57/dqc_reference/reference_markers.fasta -out GCA_945862235.1_MH-08apr19-81_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:44,347] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:44,351] [INFO] Selected 32 target genomes.
[2023-06-08 03:42:44,351] [INFO] Target genome list was writen to GCA_945862235.1_MH-08apr19-81_genomic.fna/target_genomes.txt
[2023-06-08 03:42:44,356] [INFO] Task started: fastANI
[2023-06-08 03:42:44,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg1746376b-c1d0-45ca-92b2-333d38f87354/GCA_945862235.1_MH-08apr19-81_genomic.fna.gz --refList GCA_945862235.1_MH-08apr19-81_genomic.fna/target_genomes.txt --output GCA_945862235.1_MH-08apr19-81_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:43:14,554] [INFO] Task succeeded: fastANI
[2023-06-08 03:43:14,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74fe3476-c3a2-4aa1-a081-d06778663a57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:43:14,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74fe3476-c3a2-4aa1-a081-d06778663a57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:43:14,566] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:43:14,566] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 03:43:14,567] [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
Anatilimnocola aggregata	strain=ETA_A8	GCA_007747655.1	2528021	2528021	type	True	76.2217	96	2101	95	below_threshold
Schlesneria paludicola	strain=DSM 18645	GCA_000255655.1	360056	360056	type	True	75.7804	168	2101	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.6677	100	2101	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.6519	110	2101	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.1735	57	2101	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.1604	63	2101	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	75.1575	57	2101	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.0505	72	2101	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	74.6462	58	2101	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 03:43:14,568] [INFO] DFAST Taxonomy check result was written to GCA_945862235.1_MH-08apr19-81_genomic.fna/tc_result.tsv
[2023-06-08 03:43:14,568] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:43:14,569] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:43:14,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74fe3476-c3a2-4aa1-a081-d06778663a57/dqc_reference/checkm_data
[2023-06-08 03:43:14,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:43:14,632] [INFO] Task started: CheckM
[2023-06-08 03:43:14,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945862235.1_MH-08apr19-81_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945862235.1_MH-08apr19-81_genomic.fna/checkm_input GCA_945862235.1_MH-08apr19-81_genomic.fna/checkm_result
[2023-06-08 03:44:13,962] [INFO] Task succeeded: CheckM
[2023-06-08 03:44:13,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:44:13,987] [INFO] ===== Completeness check finished =====
[2023-06-08 03:44:13,987] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:44:13,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945862235.1_MH-08apr19-81_genomic.fna/markers.fasta)
[2023-06-08 03:44:13,988] [INFO] Task started: Blastn
[2023-06-08 03:44:13,988] [INFO] Running command: blastn -query GCA_945862235.1_MH-08apr19-81_genomic.fna/markers.fasta -db /var/lib/cwl/stg74fe3476-c3a2-4aa1-a081-d06778663a57/dqc_reference/reference_markers_gtdb.fasta -out GCA_945862235.1_MH-08apr19-81_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:44:14,801] [INFO] Task succeeded: Blastn
[2023-06-08 03:44:14,807] [INFO] Selected 34 target genomes.
[2023-06-08 03:44:14,807] [INFO] Target genome list was writen to GCA_945862235.1_MH-08apr19-81_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:44:14,823] [INFO] Task started: fastANI
[2023-06-08 03:44:14,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg1746376b-c1d0-45ca-92b2-333d38f87354/GCA_945862235.1_MH-08apr19-81_genomic.fna.gz --refList GCA_945862235.1_MH-08apr19-81_genomic.fna/target_genomes_gtdb.txt --output GCA_945862235.1_MH-08apr19-81_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:44:45,408] [INFO] Task succeeded: fastANI
[2023-06-08 03:44:45,433] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 03:44:45,434] [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_003669125.1	s__SXKJ01 sp003669125	79.8642	232	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.07	98.94	0.92	0.91	3	-
GCA_005798445.1	s__SXKJ01 sp005798445	77.0951	252	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.80	99.80	0.90	0.90	2	-
GCA_016235885.1	s__JACRIH01 sp016235885	76.4906	199	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACRIH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903840265.1	s__Schlesneria sp903840265	76.4344	271	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.98	99.98	0.97	0.97	3	-
GCA_018242525.1	s__Schlesneria sp018242525	76.0453	268	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822855.1	s__Planctopirus sp013822855	76.0175	113	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctopirus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903899985.1	s__Schlesneria sp903899985	75.8414	115	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.71	99.71	0.95	0.95	2	-
GCA_903871875.1	s__Schlesneria sp903871875	75.8087	169	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.94	99.93	0.97	0.97	4	-
GCF_000255655.1	s__Schlesneria paludicola	75.7804	168	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904835.1	s__Schlesneria sp903904835	75.7225	129	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	98.97	98.46	0.92	0.88	7	-
GCA_011368275.1	s__DSVQ01 sp011368275	75.6991	105	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__DSVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	75.6581	101	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.6415	104	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	75.2889	91	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCA_016793115.1	s__PNKZ01 sp016793115	75.2337	100	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PNKZ01;g__PNKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861195.1	s__UBA10511 sp903861195	75.169	87	2101	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__UBA10511	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:44:45,436] [INFO] GTDB search result was written to GCA_945862235.1_MH-08apr19-81_genomic.fna/result_gtdb.tsv
[2023-06-08 03:44:45,436] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:44:45,440] [INFO] DFAST_QC result json was written to GCA_945862235.1_MH-08apr19-81_genomic.fna/dqc_result.json
[2023-06-08 03:44:45,440] [INFO] DFAST_QC completed!
[2023-06-08 03:44:45,440] [INFO] Total running time: 0h2m23s