[2024-01-24 15:01:23,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:23,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:23,209] [INFO] DQC Reference Directory: /var/lib/cwl/stgc70463df-99df-4ad1-841f-132d5da74683/dqc_reference
[2024-01-24 15:01:24,580] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:24,581] [INFO] Task started: Prodigal
[2024-01-24 15:01:24,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg20410851-c8c8-4d72-bc41-189e35e82b39/GCF_900199635.1_PRJEB19460_genomic.fna.gz | prodigal -d GCF_900199635.1_PRJEB19460_genomic.fna/cds.fna -a GCF_900199635.1_PRJEB19460_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:33,539] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:33,540] [INFO] Task started: HMMsearch
[2024-01-24 15:01:33,540] [INFO] Running command: hmmsearch --tblout GCF_900199635.1_PRJEB19460_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc70463df-99df-4ad1-841f-132d5da74683/dqc_reference/reference_markers.hmm GCF_900199635.1_PRJEB19460_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:33,882] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:33,885] [INFO] Found 6/6 markers.
[2024-01-24 15:01:33,916] [INFO] Query marker FASTA was written to GCF_900199635.1_PRJEB19460_genomic.fna/markers.fasta
[2024-01-24 15:01:33,917] [INFO] Task started: Blastn
[2024-01-24 15:01:33,917] [INFO] Running command: blastn -query GCF_900199635.1_PRJEB19460_genomic.fna/markers.fasta -db /var/lib/cwl/stgc70463df-99df-4ad1-841f-132d5da74683/dqc_reference/reference_markers.fasta -out GCF_900199635.1_PRJEB19460_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:34,751] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:34,755] [INFO] Selected 18 target genomes.
[2024-01-24 15:01:34,755] [INFO] Target genome list was writen to GCF_900199635.1_PRJEB19460_genomic.fna/target_genomes.txt
[2024-01-24 15:01:34,786] [INFO] Task started: fastANI
[2024-01-24 15:01:34,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg20410851-c8c8-4d72-bc41-189e35e82b39/GCF_900199635.1_PRJEB19460_genomic.fna.gz --refList GCF_900199635.1_PRJEB19460_genomic.fna/target_genomes.txt --output GCF_900199635.1_PRJEB19460_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:46,953] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:46,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc70463df-99df-4ad1-841f-132d5da74683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:46,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc70463df-99df-4ad1-841f-132d5da74683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:46,965] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:01:46,966] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:46,966] [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
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	100.0	1044	1045	95	conclusive
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	78.7543	315	1045	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_025146135.1	169435	169435	type	True	78.6775	222	1045	95	below_threshold
Provencibacterium massiliense	strain=Marseille-P2780	GCA_900169495.1	1841868	1841868	type	True	78.6285	212	1045	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	78.6236	223	1045	95	below_threshold
Phocea massiliensis	strain=Marseille-P2769	GCA_900104615.1	1841867	1841867	type	True	77.8873	86	1045	95	below_threshold
Marasmitruncus massiliensis	strain=Marseille-P3646	GCA_900186535.1	1944642	1944642	type	True	77.4876	116	1045	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	77.4871	190	1045	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.3145	74	1045	95	below_threshold
Feifania hominis	strain=BX7	GCA_014384765.1	2763660	2763660	type	True	77.24	96	1045	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.2475	80	1045	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	75.181	75	1045	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	75.1757	67	1045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:46,968] [INFO] DFAST Taxonomy check result was written to GCF_900199635.1_PRJEB19460_genomic.fna/tc_result.tsv
[2024-01-24 15:01:46,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:46,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:46,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc70463df-99df-4ad1-841f-132d5da74683/dqc_reference/checkm_data
[2024-01-24 15:01:46,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:47,002] [INFO] Task started: CheckM
[2024-01-24 15:01:47,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900199635.1_PRJEB19460_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900199635.1_PRJEB19460_genomic.fna/checkm_input GCF_900199635.1_PRJEB19460_genomic.fna/checkm_result
[2024-01-24 15:02:18,704] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:18,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:18,734] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:18,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:18,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900199635.1_PRJEB19460_genomic.fna/markers.fasta)
[2024-01-24 15:02:18,736] [INFO] Task started: Blastn
[2024-01-24 15:02:18,736] [INFO] Running command: blastn -query GCF_900199635.1_PRJEB19460_genomic.fna/markers.fasta -db /var/lib/cwl/stgc70463df-99df-4ad1-841f-132d5da74683/dqc_reference/reference_markers_gtdb.fasta -out GCF_900199635.1_PRJEB19460_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:20,139] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:20,145] [INFO] Selected 14 target genomes.
[2024-01-24 15:02:20,145] [INFO] Target genome list was writen to GCF_900199635.1_PRJEB19460_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:20,209] [INFO] Task started: fastANI
[2024-01-24 15:02:20,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg20410851-c8c8-4d72-bc41-189e35e82b39/GCF_900199635.1_PRJEB19460_genomic.fna.gz --refList GCF_900199635.1_PRJEB19460_genomic.fna/target_genomes_gtdb.txt --output GCF_900199635.1_PRJEB19460_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:27,592] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:27,603] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:27,604] [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_900199635.1	s__Anaerotruncus massiliensis	100.0	1044	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	conclusive
GCF_900078395.1	s__Anaerotruncus rubiinfantis	78.7543	315	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.23	99.21	0.89	0.86	5	-
GCF_000154565.1	s__Anaerotruncus colihominis	78.6306	224	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.95	97.75	0.87	0.80	16	-
GCA_019114825.1	s__Anaerotruncus excrementipullorum	78.4304	206	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.88	99.88	0.94	0.94	2	-
GCF_010206195.1	s__Anaerotruncus colihominis_A	77.8724	223	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.98	98.75	0.89	0.87	3	-
GCA_004340125.1	s__Harryflintia acetispora	77.644	210	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Harryflintia	95.0	98.73	98.54	0.92	0.90	6	-
GCA_014384885.1	s__Hydrogenoanaerobacterium sp014384885	77.4709	191	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	98.59	98.59	0.91	0.91	2	-
GCA_910585525.1	s__Angelakisella sp910585525	77.2289	114	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904398655.1	s__Anaerotruncus sp904398655	77.1693	125	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904398325.1	s__Neoruminococcus faecicola	77.1529	92	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Neoruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113125.1	s__Pygmaiobacter gallistercoris	76.9909	77	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pygmaiobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586875.1	s__Anaerotruncus sp910586875	76.7044	96	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554485.1	s__Angelakisella sp004554485	76.3563	65	1045	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	97.18	96.00	0.84	0.76	6	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:27,605] [INFO] GTDB search result was written to GCF_900199635.1_PRJEB19460_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:27,606] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:27,609] [INFO] DFAST_QC result json was written to GCF_900199635.1_PRJEB19460_genomic.fna/dqc_result.json
[2024-01-24 15:02:27,609] [INFO] DFAST_QC completed!
[2024-01-24 15:02:27,610] [INFO] Total running time: 0h1m4s