[2024-01-24 13:49:55,629] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,632] [INFO] DQC Reference Directory: /var/lib/cwl/stge8a7eab1-0992-44dc-bf32-cf9a104ed649/dqc_reference
[2024-01-24 13:49:56,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,896] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg50a0cd9e-016f-4886-87a1-44b59f7016da/GCF_019239235.1_ASM1923923v1_genomic.fna.gz | prodigal -d GCF_019239235.1_ASM1923923v1_genomic.fna/cds.fna -a GCF_019239235.1_ASM1923923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:18,106] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:18,106] [INFO] Task started: HMMsearch
[2024-01-24 13:50:18,106] [INFO] Running command: hmmsearch --tblout GCF_019239235.1_ASM1923923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8a7eab1-0992-44dc-bf32-cf9a104ed649/dqc_reference/reference_markers.hmm GCF_019239235.1_ASM1923923v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:18,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:18,416] [INFO] Found 6/6 markers.
[2024-01-24 13:50:18,455] [INFO] Query marker FASTA was written to GCF_019239235.1_ASM1923923v1_genomic.fna/markers.fasta
[2024-01-24 13:50:18,456] [INFO] Task started: Blastn
[2024-01-24 13:50:18,456] [INFO] Running command: blastn -query GCF_019239235.1_ASM1923923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8a7eab1-0992-44dc-bf32-cf9a104ed649/dqc_reference/reference_markers.fasta -out GCF_019239235.1_ASM1923923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:19,079] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:19,083] [INFO] Selected 24 target genomes.
[2024-01-24 13:50:19,083] [INFO] Target genome list was writen to GCF_019239235.1_ASM1923923v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:19,091] [INFO] Task started: fastANI
[2024-01-24 13:50:19,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg50a0cd9e-016f-4886-87a1-44b59f7016da/GCF_019239235.1_ASM1923923v1_genomic.fna.gz --refList GCF_019239235.1_ASM1923923v1_genomic.fna/target_genomes.txt --output GCF_019239235.1_ASM1923923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:33,250] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:33,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8a7eab1-0992-44dc-bf32-cf9a104ed649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:33,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8a7eab1-0992-44dc-bf32-cf9a104ed649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:33,269] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:33,269] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:33,270] [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
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	78.8035	152	1175	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	78.718	295	1175	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	78.6758	279	1175	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	78.6544	318	1175	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	78.598	290	1175	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	78.5745	321	1175	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	78.5597	322	1175	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	78.5277	321	1175	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	78.5208	285	1175	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	78.5149	316	1175	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	78.4618	295	1175	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	78.4482	290	1175	95	below_threshold
Bacteroides fragilis	strain=CCUG4856T	GCA_005706655.1	817	817	type	True	78.4237	142	1175	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.4145	155	1175	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	78.4131	145	1175	95	below_threshold
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	78.3601	138	1175	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	78.3364	142	1175	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_000025985.1	817	817	type	True	78.2929	146	1175	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.262	156	1175	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	78.2061	150	1175	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	78.1999	152	1175	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	78.1274	233	1175	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	78.1153	153	1175	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_000169015.1	47678	47678	suspected-type	True	78.0722	151	1175	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:33,271] [INFO] DFAST Taxonomy check result was written to GCF_019239235.1_ASM1923923v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:33,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:33,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:33,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8a7eab1-0992-44dc-bf32-cf9a104ed649/dqc_reference/checkm_data
[2024-01-24 13:50:33,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:33,314] [INFO] Task started: CheckM
[2024-01-24 13:50:33,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019239235.1_ASM1923923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019239235.1_ASM1923923v1_genomic.fna/checkm_input GCF_019239235.1_ASM1923923v1_genomic.fna/checkm_result
[2024-01-24 13:51:30,300] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:30,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:30,323] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:30,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:30,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019239235.1_ASM1923923v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:30,324] [INFO] Task started: Blastn
[2024-01-24 13:51:30,324] [INFO] Running command: blastn -query GCF_019239235.1_ASM1923923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8a7eab1-0992-44dc-bf32-cf9a104ed649/dqc_reference/reference_markers_gtdb.fasta -out GCF_019239235.1_ASM1923923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:31,193] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:31,197] [INFO] Selected 12 target genomes.
[2024-01-24 13:51:31,197] [INFO] Target genome list was writen to GCF_019239235.1_ASM1923923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:31,219] [INFO] Task started: fastANI
[2024-01-24 13:51:31,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg50a0cd9e-016f-4886-87a1-44b59f7016da/GCF_019239235.1_ASM1923923v1_genomic.fna.gz --refList GCF_019239235.1_ASM1923923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019239235.1_ASM1923923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:40,518] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:40,535] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:40,535] [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_900130135.1	s__Bacteroides togonis	97.4053	958	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	conclusive
GCA_019116805.1	s__Bacteroides merdavium	87.5514	672	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128475.1	s__Bacteroides massiliensis	86.3163	722	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCF_900108345.1	s__Bacteroides ndongoniae	81.2295	470	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
GCA_900553815.1	s__Bacteroides sp900553815	80.4421	332	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.95	97.95	0.73	0.73	2	-
GCA_905201685.1	s__Bacteroides sp905201685	80.0118	201	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883785.1	s__Bacteroides intestinipullorum	78.9851	245	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374365.1	s__Bacteroides gallinarum	78.6203	289	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_017471925.1	s__Bacteroides sp017471925	78.5705	263	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154205.1	s__Bacteroides uniformis	78.5344	320	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_000154525.1	s__Bacteroides stercoris	78.4715	296	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_002160055.1	s__Bacteroides avicola	78.4058	270	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.46	98.46	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:40,537] [INFO] GTDB search result was written to GCF_019239235.1_ASM1923923v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:40,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:40,548] [INFO] DFAST_QC result json was written to GCF_019239235.1_ASM1923923v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:40,548] [INFO] DFAST_QC completed!
[2024-01-24 13:51:40,548] [INFO] Total running time: 0h1m45s