[2023-06-26 23:16:07,504] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:16:07,506] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:16:07,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d63f8d1-a4ed-46c5-af47-46be37c1e087/dqc_reference
[2023-06-26 23:16:08,731] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:16:08,732] [INFO] Task started: Prodigal
[2023-06-26 23:16:08,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ac821f2-e127-4bec-8876-490510c6065b/GCA_026003015.1_ASM2600301v1_genomic.fna.gz | prodigal -d GCA_026003015.1_ASM2600301v1_genomic.fna/cds.fna -a GCA_026003015.1_ASM2600301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:16:14,119] [INFO] Task succeeded: Prodigal
[2023-06-26 23:16:14,120] [INFO] Task started: HMMsearch
[2023-06-26 23:16:14,120] [INFO] Running command: hmmsearch --tblout GCA_026003015.1_ASM2600301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d63f8d1-a4ed-46c5-af47-46be37c1e087/dqc_reference/reference_markers.hmm GCA_026003015.1_ASM2600301v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:16:14,289] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:16:14,290] [INFO] Found 6/6 markers.
[2023-06-26 23:16:14,314] [INFO] Query marker FASTA was written to GCA_026003015.1_ASM2600301v1_genomic.fna/markers.fasta
[2023-06-26 23:16:14,314] [INFO] Task started: Blastn
[2023-06-26 23:16:14,314] [INFO] Running command: blastn -query GCA_026003015.1_ASM2600301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d63f8d1-a4ed-46c5-af47-46be37c1e087/dqc_reference/reference_markers.fasta -out GCA_026003015.1_ASM2600301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:16:15,103] [INFO] Task succeeded: Blastn
[2023-06-26 23:16:15,107] [INFO] Selected 25 target genomes.
[2023-06-26 23:16:15,107] [INFO] Target genome list was writen to GCA_026003015.1_ASM2600301v1_genomic.fna/target_genomes.txt
[2023-06-26 23:16:15,110] [INFO] Task started: fastANI
[2023-06-26 23:16:15,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ac821f2-e127-4bec-8876-490510c6065b/GCA_026003015.1_ASM2600301v1_genomic.fna.gz --refList GCA_026003015.1_ASM2600301v1_genomic.fna/target_genomes.txt --output GCA_026003015.1_ASM2600301v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:16:39,559] [INFO] Task succeeded: fastANI
[2023-06-26 23:16:39,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d63f8d1-a4ed-46c5-af47-46be37c1e087/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:16:39,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d63f8d1-a4ed-46c5-af47-46be37c1e087/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:16:39,577] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:16:39,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:16:39,577] [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
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.4417	145	732	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	75.4228	133	732	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	75.4136	158	732	95	below_threshold
Sanguibacter gelidistatuariae	strain=ISLP-3	GCA_900096585.1	1814289	1814289	type	True	75.4089	88	732	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	75.4083	120	732	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_014191255.1	941986	941986	type	True	75.2914	151	732	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.2906	139	732	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	75.2873	156	732	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	75.2541	141	732	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	75.2514	154	732	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_007713755.1	941986	941986	type	True	75.2398	152	732	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	75.2322	112	732	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	75.1895	115	732	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	75.167	191	732	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	75.1449	184	732	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	75.1445	120	732	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	75.093	164	732	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	75.0791	181	732	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	75.0283	204	732	95	below_threshold
Frankia irregularis	strain=DSM 45899	GCA_001536285.1	795642	795642	type	True	75.0098	145	732	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.8951	169	732	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	74.6838	65	732	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:16:39,586] [INFO] DFAST Taxonomy check result was written to GCA_026003015.1_ASM2600301v1_genomic.fna/tc_result.tsv
[2023-06-26 23:16:39,586] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:16:39,586] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:16:39,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d63f8d1-a4ed-46c5-af47-46be37c1e087/dqc_reference/checkm_data
[2023-06-26 23:16:39,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:16:39,612] [INFO] Task started: CheckM
[2023-06-26 23:16:39,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026003015.1_ASM2600301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026003015.1_ASM2600301v1_genomic.fna/checkm_input GCA_026003015.1_ASM2600301v1_genomic.fna/checkm_result
[2023-06-26 23:17:06,746] [INFO] Task succeeded: CheckM
[2023-06-26 23:17:06,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:17:06,762] [INFO] ===== Completeness check finished =====
[2023-06-26 23:17:06,762] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:17:06,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026003015.1_ASM2600301v1_genomic.fna/markers.fasta)
[2023-06-26 23:17:06,762] [INFO] Task started: Blastn
[2023-06-26 23:17:06,762] [INFO] Running command: blastn -query GCA_026003015.1_ASM2600301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d63f8d1-a4ed-46c5-af47-46be37c1e087/dqc_reference/reference_markers_gtdb.fasta -out GCA_026003015.1_ASM2600301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:17:07,918] [INFO] Task succeeded: Blastn
[2023-06-26 23:17:07,923] [INFO] Selected 17 target genomes.
[2023-06-26 23:17:07,923] [INFO] Target genome list was writen to GCA_026003015.1_ASM2600301v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:17:07,934] [INFO] Task started: fastANI
[2023-06-26 23:17:07,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ac821f2-e127-4bec-8876-490510c6065b/GCA_026003015.1_ASM2600301v1_genomic.fna.gz --refList GCA_026003015.1_ASM2600301v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026003015.1_ASM2600301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:17:16,432] [INFO] Task succeeded: fastANI
[2023-06-26 23:17:16,444] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:17:16,444] [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_004366195.1	s__HRBIN12 sp004366195	78.1001	233	732	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__UBA4738;f__HRBIN12;g__HRBIN12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054185.1	s__DSJA01 sp011054185	77.9795	287	732	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__UBA4738;f__HRBIN12;g__DSJA01	95.0	99.28	99.28	0.88	0.88	2	-
GCA_005884925.1	s__AC-51 sp005884925	77.8607	238	732	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__UBA4738;f__HRBIN12;g__AC-51	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331385.1	s__DSRY01 sp011331385	77.82	306	732	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__UBA4738;f__HRBIN12;g__DSRY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883885.1	s__AC-51 sp005883885	77.7587	189	732	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__UBA4738;f__HRBIN12;g__AC-51	95.0	96.91	96.91	0.75	0.75	2	-
GCA_005885035.1	s__AC-51 sp005885035	77.5107	242	732	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__UBA4738;f__HRBIN12;g__AC-51	95.0	99.11	98.97	0.90	0.89	4	-
GCA_005885325.1	s__AC-69 sp005885325	77.1661	150	732	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__UBA4738;f__HRBIN12;g__AC-69	95.0	98.32	98.32	0.78	0.78	2	-
GCA_002413305.1	s__UBA4738 sp002413305	76.2394	93	732	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__UBA4738;f__UBA4738;g__UBA4738	95.0	99.61	99.56	0.84	0.82	3	-
GCA_005888465.1	s__AC-55 sp005888465	76.1748	120	732	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__UBA4738;f__UBA4738;g__AC-55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377835.1	s__WHTG01 sp009377835	75.6272	67	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__WHTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255565.1	s__RAAP-2 sp002255565	75.4598	81	732	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862555.1	s__Asanoa siamensis	75.1561	194	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018606725.1	s__JAGYID01 sp018606725	74.9896	71	732	d__Bacteria;p__Acidobacteriota;c__Mor1;o__Gp22-AA2;f__Gp22-AA2;g__JAGYID01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479655.1	s__CAJQNK01 sp905479655	74.9503	84	732	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__CAJQNK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:17:16,446] [INFO] GTDB search result was written to GCA_026003015.1_ASM2600301v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:17:16,447] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:17:16,451] [INFO] DFAST_QC result json was written to GCA_026003015.1_ASM2600301v1_genomic.fna/dqc_result.json
[2023-06-26 23:17:16,451] [INFO] DFAST_QC completed!
[2023-06-26 23:17:16,451] [INFO] Total running time: 0h1m9s